2YBD

Crystal structure of probable had family hydrolase from pseudomonas fluorescens pf-5 with bound phosphate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5		PROTEIN (10MM HEPES PH 7.5, 150 MM NACL, 10% GLYCEROL, 5 MM DTT, 5 MM MGCL);RESERVOUR (2.5 M NA/K PHOSPHATE, 150 MM NACITRATE, PH 5.0;CRYOPROTECTION (1.8 M NA/K PHOSPHATE, 100 MM NACITRATE, 18.5% GLYCEROL, 185 MM MGSO4) TWO MINUTE SOAK.

Crystal Properties
Matthews coefficient	Solvent content
3.5	65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.978	α = 90
b = 65.978	β = 90
c = 250.4	γ = 120

Symmetry
Space Group	P 61 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	93	IMAGE PLATE	RIGAKU-MSC RAXIS IV	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	40	98.5	0.08	32.6	15.3		22605			22.11

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	2.03	89.2		0.3	6.4	6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3M9L	2.001	32.989	21908	1106	95.89	0.173	0.1707	0.2177

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]
0.8479			0.8479		-1.6957

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.246
f_angle_d	1.032
f_chiral_restr	0.071
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1507
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	11

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	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 R01GM133198.