4DLL | pdb_00004dll

Crystal structure of a 2-hydroxy-3-oxopropionate reductase from Polaromonas sp. JS666

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VPD	pdb entry 1VPD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.2M NaCl, 0.1M Bis-tris pH 6.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.868	α = 92.14
b = 47.01	β = 95.3
c = 77.498	γ = 101.19

Symmetry
Space Group	P 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 315	mirrors	2012-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9791	NSLS	X29A

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	2.11	50	93.6	0.06	8.6	3.1	29628	29628

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	2.11	2.19	77.4		0.3	2.5	2.8	2422

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 1VPD	2.11	38.52	29628	28107	1484	93.76	0.22133	0.21819	0.22	0.27825	0.28	RANDOM	39.573

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]
0.04	0.05	0.08	-0.05	0.03	0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.681
r_dihedral_angle_3_deg	17.972
r_dihedral_angle_4_deg	17.799
r_dihedral_angle_1_deg	7.246
r_scangle_it	4.862
r_scbond_it	3.323
r_angle_refined_deg	1.882
r_mcangle_it	1.657
r_mcbond_it	0.912
r_chiral_restr	0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.681
r_dihedral_angle_3_deg	17.972
r_dihedral_angle_4_deg	17.799
r_dihedral_angle_1_deg	7.246
r_scangle_it	4.862
r_scbond_it	3.323
r_angle_refined_deg	1.882
r_mcangle_it	1.657
r_mcbond_it	0.912
r_chiral_restr	0.122
r_bond_refined_d	0.02
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4115
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	10

Software

Software
Software Name	Purpose
CBASS	data collection
MOLREP	phasing
PHASER	phasing
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.