2QEE | pdb_00002qee

Crystal structure of putative amidohydrolase BH0493 from Bacillus halodurans C-125

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q08	PDB entry 2Q08

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	294	0.1M Bis-Tris pH 6.5, 45% PPG P 400 (INDEX E10), VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.995	α = 78.85
b = 122.208	β = 78.95
c = 127.582	γ = 80.92

Symmetry
Space Group	P 1

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	SGX-CAT	2007-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97900	APS	31-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	1.65	50	88.5	0.044	12.6	2.1		759838

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)
	1.65	1.71	49.1		0.384		1.5	42180

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 2Q08	1.65	19.99	759011	37962	89.62	0.189	0.187	0.1866	0.224	0.2231	RANDOM	26.888

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.476
r_dihedral_angle_4_deg	18.91
r_dihedral_angle_3_deg	13.342
r_scbond_it	6.861
r_dihedral_angle_1_deg	6.402
r_scangle_it	4.416
r_mcangle_it	3.734
r_angle_refined_deg	1.604
r_mcbond_it	1.456
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.476
r_dihedral_angle_4_deg	18.91
r_dihedral_angle_3_deg	13.342
r_scbond_it	6.861
r_dihedral_angle_1_deg	6.402
r_scangle_it	4.416
r_mcangle_it	3.734
r_angle_refined_deg	1.604
r_mcbond_it	1.456
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.214
r_metal_ion_refined	0.187
r_symmetry_hbond_refined	0.159
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.116
r_bond_refined_d	0.018
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	41373
Nucleic Acid Atoms
Solvent Atoms	4909
Heterogen Atoms	32

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing

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.