4OVY

Crystal structure of Haloacid dehalogenase domain protein hydrolase from Planctomyces limnophilus DSM 3776

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	297	1.8 M Tris-Ammonium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.95	α = 90
b = 75.502	β = 90
c = 64.357	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	ADSC QUANTUM 315r		2012-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97899	APS	19-ID

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	50	99.9	0.077	10	5.7		33799		-3

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	1.83	99.9		0.947		5.1	1657

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.8	29.62	30734	1551	90.79	0.1332	0.1309	0.1746	RANDOM	27.062

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]
-0.07			-1.72		1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.819
r_sphericity_free	30.554
r_dihedral_angle_3_deg	11.381
r_sphericity_bonded	10.653
r_dihedral_angle_4_deg	10.183
r_dihedral_angle_1_deg	5.243
r_rigid_bond_restr	1.497
r_angle_refined_deg	1.103
r_angle_other_deg	0.723
r_chiral_restr	0.066

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.819
r_sphericity_free	30.554
r_dihedral_angle_3_deg	11.381
r_sphericity_bonded	10.653
r_dihedral_angle_4_deg	10.183
r_dihedral_angle_1_deg	5.243
r_rigid_bond_restr	1.497
r_angle_refined_deg	1.103
r_angle_other_deg	0.723
r_chiral_restr	0.066
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2446
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	51

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.