2NQW | pdb_00002nqw

Structure of the transporter associated domain from PG_0272, a CBS domain protein from Porphyromonas gingivalis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.5	291	0.1M citric acid, 25% PEG 3350, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.733	α = 90
b = 45.195	β = 90
c = 57.214	γ = 90

Symmetry
Space Group	P 21 21 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	CUSTOM-MADE		2006-10-29	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97910, 0.97929	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	24.2	94.6	0.068	11.6	7.8	20972	20972		-3	16.11

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.33	69		0.264	3.6	3.6

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 (All)	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	MAD	THROUGHOUT	1.3	24.17	19898	19898	1072	94.63	0.13157	0.13157	0.12978	0.13	0.16715	0.17	RANDOM	15.998

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]
1.31			-0.71		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.537
r_dihedral_angle_3_deg	10.925
r_dihedral_angle_4_deg	10.869
r_sphericity_free	7.207
r_dihedral_angle_1_deg	6.415
r_scangle_it	4.834
r_sphericity_bonded	4.655
r_scbond_it	3.381
r_mcangle_it	2.196
r_rigid_bond_restr	2.022
r_mcbond_it	1.712
r_angle_refined_deg	1.601
r_nbtor_refined	0.319
r_symmetry_vdw_refined	0.27
r_symmetry_hbond_refined	0.262
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	709
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building