4LVU | pdb_00004lvu

Crystal Structure of a Putative Short Chain Dehydrogenase from Burkholderia thailandensis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JRO	PDB ENTRY 4JRO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	JCSG+(a5): 20% PEG3350, 200 mM magnesium formate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.46	α = 90
b = 103.39	β = 90
c = 71.29	γ = 90

Symmetry
Space Group	P 21 21 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	beryllium lenses	2013-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9786	APS	21-ID-F

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	1.25	50	98	0.05	26.37	9.8	146259	143334		-3	14.702

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	1.25	1.28	94.6		0.456	4.07

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 4JRO	1.25	45.4	143334	143283	7172	98.05	0.1181	0.1181	0.1168	0.1158	0.141	0.1406	RANDOM	13.3299

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_sphericity_free	40.918
r_dihedral_angle_2_deg	34.421
r_dihedral_angle_4_deg	12.222
r_dihedral_angle_3_deg	11.858
r_sphericity_bonded	9.675
r_dihedral_angle_1_deg	5.337
r_rigid_bond_restr	1.578
r_mcangle_it	1.408
r_angle_refined_deg	1.357
r_mcbond_it	1.117
r_mcbond_other	1.111
r_angle_other_deg	0.785
r_chiral_restr	0.088
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3697
Nucleic Acid Atoms
Solvent Atoms	671
Heterogen Atoms	8

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling