3R3X | pdb_00003r3x

Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Bromoacetate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	15-24% PEG3350, 0.1-0.2M CaCl2 and 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.26	α = 90
b = 80.17	β = 103.19
c = 85.54	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		IMAGE PLATE	MAR scanner 345 mm plate		2009-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.8	83.33	95.9	0.055	18.95			49450		-3	22.044

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	1.8	1.85	92.8		0.411	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	1.8	19.76	49450	2498	95.94	0.1921	0.1898	0.2	0.2336	0.24	RANDOM	14.6455

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]
0.33		0.39	0.37		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.723
r_dihedral_angle_4_deg	17.659
r_dihedral_angle_3_deg	14.698
r_dihedral_angle_1_deg	6.485
r_scangle_it	4.161
r_scbond_it	2.735
r_angle_refined_deg	1.79
r_mcangle_it	1.708
r_angle_other_deg	1.075
r_mcbond_it	1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.723
r_dihedral_angle_4_deg	17.659
r_dihedral_angle_3_deg	14.698
r_dihedral_angle_1_deg	6.485
r_scangle_it	4.161
r_scbond_it	2.735
r_angle_refined_deg	1.79
r_mcangle_it	1.708
r_angle_other_deg	1.075
r_mcbond_it	1.05
r_mcbond_other	0.343
r_chiral_restr	0.112
r_bond_refined_d	0.022
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4622
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	11

Software

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