2GAU | pdb_00002gau

Crystal structure of transcriptional regulator, Crp/Fnr family from Porphyromonas gingivalis (APC80792), Structural genomics, MCSG

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	0.1M succinic acid, 15% PEG 3350 , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.723	α = 90
b = 76.723	β = 90
c = 86.32	γ = 90

Symmetry
Space Group	P 41 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 315	horizontal-focussing Si-111 double-crystal monochromator and vertical-focussing mirror	2005-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97932	APS	19-ID

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	1.9	57.354	98.6	0.115	25.4	14.8	20940	20641	1	1	35.5

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	1.9	1.97	91.5		0.897	1.42	5.4	1881

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	SAD	THROUGHOUT	1.9	57.35	20641	19581	1060	98.58	0.211	0.21058	0.20805	0.21	0.25837	0.26	RANDOM	28.585

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]
-0.46			-0.46		0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.529
r_dihedral_angle_4_deg	22.331
r_dihedral_angle_3_deg	13.747
r_dihedral_angle_1_deg	5.578
r_scangle_it	3.074
r_scbond_it	2.013
r_angle_refined_deg	1.221
r_mcangle_it	1.149
r_mcbond_it	0.717
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.529
r_dihedral_angle_4_deg	22.331
r_dihedral_angle_3_deg	13.747
r_dihedral_angle_1_deg	5.578
r_scangle_it	3.074
r_scbond_it	2.013
r_angle_refined_deg	1.221
r_mcangle_it	1.149
r_mcbond_it	0.717
r_nbtor_refined	0.301
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.199
r_symmetry_vdw_refined	0.195
r_symmetry_hbond_refined	0.173
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1742
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
O	model building
Coot	model building
CCP4	phasing
ARP/wARP	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.