2P8C | pdb_00002p8c

Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579 complexed with N-succinyl Arg.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P88	PDB entry 2P88

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	293	35% MPD, 0.1 M Na/K phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.339	α = 90
b = 137.339	β = 90
c = 87.85	γ = 90

Symmetry
Space Group	I 4 2 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 4	mirrors	2006-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.97915	NSLS	X4A

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	25	93.9	0.098		12.7	26872	26872			17.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2P88	2	24.67	26872	26872	1318	93.9	0.18	0.18	0.18	0.17	0.199	0.19	RANDOM	29.5

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]
-4.23			-4.23		8.45

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.7
c_scangle_it	2.97
c_scbond_it	2.16
c_mcangle_it	1.64
c_angle_deg	1.2
c_mcbond_it	1.09
c_improper_angle_d	0.77
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2871
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	20

Software

Software
Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
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.