3GEI | pdb_00003gei

Crystal structure of MnmE from Chlorobium tepidum in complex with GCP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XZP	PDB ENTRY 1XZP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	100mM MES, 46mM NaOH, 12% PEG 4000, 40mM NaCl, 5mM GCP, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.93	68.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.882	α = 90
b = 224.572	β = 90
c = 156.788	γ = 90

Symmetry
Space Group	C 2 2 21

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	MAR CCD 165 mm	Mirrors	2006-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9796	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	3.4	20	99.2	0.129	0.131	12.13	7.45	34300	34042			92.53

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)
	3.4	3.425	100		0.654	2.02	7.61	719

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1XZP	3.4	19.94	32320	1721	99.25	0.24624	0.245	0.28	0.26891	0.28	RANDOM	123.559

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]
-0.81			-5.79		6.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.351
r_dihedral_angle_3_deg	18.652
r_dihedral_angle_4_deg	17.403
r_dihedral_angle_1_deg	5.607
r_scangle_it	2.106
r_angle_refined_deg	1.198
r_scbond_it	1.144
r_mcangle_it	1.005
r_mcbond_it	0.537
r_nbtor_refined	0.298
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.193
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.081
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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	8715
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	65

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling