2P10 | pdb_00002p10

CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHONOPYRUVATE HYDROLASE (MLL9387) FROM MESORHIZOBIUM LOTI MAFF303099 AT 2.15 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4	277	NANODROP, 3.0% PEG 4000, 23.3% Glycerol, 0.1M Sodium acetate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 4.00

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.269	α = 90
b = 180.269	β = 90
c = 185.514	γ = 120

Symmetry
Space Group	H 3

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 4	1M LONG RH COATED BENT CYLINDRICAL MIRROR FOR HORIZONTAL AND VERTICAL FOCUSING	2007-01-29	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL1-5	0.918381, 0.979354	SSRL	BL1-5

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	2.15	45.083	99.3	0.093	8.34	3.31		121425			37.31

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	2.15	2.23	99.6		0.764	1.6	3.28

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	MAD	THROUGHOUT	2.15	45.08	121409	6092	99.3	0.165	0.162	0.17	0.204	0.21	RANDOM	43.89

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]
0.13	0.07		0.13		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.708
r_dihedral_angle_4_deg	15.376
r_dihedral_angle_3_deg	15.134
r_scangle_it	6.594
r_dihedral_angle_1_deg	5.556
r_scbond_it	4.789
r_mcangle_it	2.283
r_mcbond_it	1.404
r_angle_refined_deg	1.249
r_angle_other_deg	0.888
r_mcbond_other	0.468
r_symmetry_vdw_other	0.274
r_nbd_refined	0.205
r_nbd_other	0.189
r_symmetry_vdw_refined	0.179
r_symmetry_hbond_refined	0.174
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.14
r_xyhbond_nbd_other	0.118
r_nbtor_other	0.086
r_chiral_restr	0.067
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12016
Nucleic Acid Atoms
Solvent Atoms	712
Heterogen Atoms	82

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing