3QVK | pdb_00003qvk

Allantoin racemase from Klebsiella pneumoniae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.9	291	30% Peg 400, 0.1 M sodium acetate pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.896	α = 90
b = 124.896	β = 90
c = 126.972	γ = 120

Symmetry
Space Group	P 63 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 315		2009-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9791	APS	24-ID-E

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	1.999	108.163	98.3	0.096	13.3	5	39452	39452	2	2

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	1.999	2.07	98.2		0.381		4.5	3866

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	FOURIER SYNTHESIS	THROUGHOUT	1.999	108.16	39452	39437	1974	98.38	0.222	0.222	0.2208	0.2215	0.2456	0.2452	RANDOM	31.954

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]
-0.71	-0.36		-0.71		1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.182
r_dihedral_angle_4_deg	13.591
r_dihedral_angle_3_deg	12.9
r_dihedral_angle_1_deg	4.43
r_angle_refined_deg	0.927
r_scangle_it	0.814
r_scbond_it	0.452
r_mcangle_it	0.367
r_mcbond_it	0.195
r_chiral_restr	0.052
r_bond_refined_d	0.005
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3534
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	22

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
SOLVE	phasing