3HUR | pdb_00003hur

Crystal structure of alanine racemase from Oenococcus oeni

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	3.5	294	100mM citric acid pH 3.5, 2.0M ammonium sulfate, vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
4.14	70.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.499	α = 90
b = 130.549	β = 90
c = 189.441	γ = 90

Symmetry
Space Group	F 2 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	MARMOSAIC 225 mm CCD		2009-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	2.5	26.762	99.9	0.097	0.097	14.7	8.3	25536	25510			53.3

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)
	2.5	2.64	100		0.365	0.365	5.3	8.3	3677

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.5	20	25492	25454	1277	99.85	0.22	0.219	0.252	0.2587	RANDOM	42.231

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]
-2.47			1.9		0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.926
r_dihedral_angle_4_deg	26.778
r_dihedral_angle_3_deg	17.603
r_dihedral_angle_1_deg	6.647
r_scangle_it	4.165
r_scbond_it	2.506
r_mcangle_it	1.75
r_angle_refined_deg	1.618
r_angle_other_deg	0.957
r_mcbond_it	0.917
r_mcbond_other	0.148
r_chiral_restr	0.096
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2966
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	15

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building