Experiment: 2YBD

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M9L	PDB ENTRY 3M9L

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3M9L	2.001	32.989	21908	1106	95.89	0.173	0.1707	0.162	0.2177	0.2079

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