3H8T | pdb_00003h8t

Structure of Porphyromonas gingivalis heme-binding protein HmuY in complex with Heme

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	Crystallization assays were performed following the sitting-drop vapor diffusion method. Reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on 96x2-well MRC plates (Wilden / Innovadyne) by a Cartesian nanodrop robot (Genomic Solutions) at the joint IBMB-CSIC/IRB/Barcelona Science Park High-Throughput Crystallography Platform (PAC). Best crystals as thin reddish prisms appeared in a Bruker steady-temperature crystal farm at 20 C using protein solution (26mg/mL in 5mM Tris/HCl, pH 8.0) and 2.4M (NH4)2SO4, 0.1M MES, pH6.0 as reservoir solution and D(+)-glucose monohydrate as additive (relative volumetric ratios 1:1:0.35). These conditions were successfully scaled up to the microliter range with Cryschem crystallization dishes (Hampton Research). VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.74	α = 90
b = 93.74	β = 90
c = 113.73	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2008-07-18	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315r		2008-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.0000	ESRF	ID23-1
2	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9792	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1,2	1.8	48.6	100	0.101	17.6	12.9	47598	47598

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.8	1.9	99.9		0.669	4.2	13.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	THROUGHOUT	1.8	48.6	47598	46847	720	99.95	0.16057	0.16015	0.32	0.18709	0.32	RANDOM	14.133

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.01			0.01		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.865
r_dihedral_angle_4_deg	16.615
r_dihedral_angle_3_deg	12.492
r_dihedral_angle_1_deg	6.633
r_scangle_it	3.608
r_scbond_it	2.188
r_mcangle_it	1.325
r_angle_refined_deg	1.31
r_mcbond_it	0.695
r_chiral_restr	0.105
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2858
Nucleic Acid Atoms
Solvent Atoms	432
Heterogen Atoms	142

Software

Software
Software Name	Purpose
ADSC	data collection
SHELXDE	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling