2QE9 | pdb_00002qe9

Crystal structure of a putative metal-dependent hydrolase (yiza, bsu10800) from bacillus subtilis at 1.90 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	277	NANODROP, 0.2M NaCl, 10.0% PEG 3000, 0.1M Phosphate Citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.184	α = 90
b = 53.184	β = 90
c = 251.364	γ = 90

Symmetry
Space Group	P 41 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2007-06-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162, 0.97925	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.9	29.761	100	0.094	0.094	5.4	6.7		29798

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95	100		0.92	0.92	0.8	6.9	2129

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	1.9	29.761	29655	1500	99.83	0.187	0.185	0.19	0.226	0.23	RANDOM	27.46

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]
-1.3			-1.3		2.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.149
r_dihedral_angle_4_deg	13.224
r_dihedral_angle_3_deg	10.904
r_scangle_it	5.67
r_scbond_it	4.402
r_dihedral_angle_1_deg	3.604
r_mcangle_it	2.608
r_mcbond_it	1.733
r_angle_refined_deg	1.429
r_angle_other_deg	1.31
r_mcbond_other	0.424
r_nbd_refined	0.188
r_symmetry_vdw_refined	0.179
r_nbtor_refined	0.167
r_nbd_other	0.139
r_symmetry_vdw_other	0.118
r_xyhbond_nbd_refined	0.099
r_symmetry_hbond_refined	0.085
r_chiral_restr	0.075
r_nbtor_other	0.072
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2716
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
SHARP	phasing