4JHM | pdb_00004jhm

Crystal structure of a putative mandelate racemase/muconate lactonizing enzyme from Pseudovibrio sp.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SJN	PDB ENTRY 3SJN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	30% PEG 8000, 100mM Imidazole/Hydrochloric acid pH 8.0, 200mM sodium chloride, Vapor diffusion, Sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 201.793	α = 90
b = 117.313	β = 99.77
c = 143.127	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 315r		2011-06-16		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.978	NSLS	X29A

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	2.8	55.536	96	0.053	0.095	8.8	3.7	77549	77549

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	92.5		0.379	0.379	2	3.4	10798

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 (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 3SJN	2.8	39.41	75912	75912	3989	98.57	0.1971	0.1941	0.2	0.253	0.25	RANDOM	85.245

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]
		-0.01	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.813
r_dihedral_angle_4_deg	16.698
r_dihedral_angle_3_deg	14.909
r_dihedral_angle_1_deg	5.162
r_mcangle_it	4.554
r_mcbond_it	3.012
r_mcbond_other	3.012
r_angle_refined_deg	0.83
r_angle_other_deg	0.581
r_chiral_restr	0.052

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.813
r_dihedral_angle_4_deg	16.698
r_dihedral_angle_3_deg	14.909
r_dihedral_angle_1_deg	5.162
r_mcangle_it	4.554
r_mcbond_it	3.012
r_mcbond_other	3.012
r_angle_refined_deg	0.83
r_angle_other_deg	0.581
r_chiral_restr	0.052
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23530
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
MOSFLM	data reduction
MOLREP	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.