2R11 | pdb_00002r11

Crystal structure of putative hydrolase (2632844) from Bacillus subtilis at 1.96 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	277	NANODROP, 14.0% PEG 8000, 0.2M MgCl2, 0.1M CHES pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.59	α = 90
b = 97.55	β = 110.01
c = 88.27	γ = 90

Symmetry
Space Group	P 1 21 1

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	2006-04-30	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837, 0.97934	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	1.96	48.795	93	0.094	0.094	6.2	2.9		85536			20.86

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)
	1.96	2.07	99.8		0.464	0.464	1.5	2.8	13370

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 (All)	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	1.96	48.795	85485	4284	92.9	0.184	0.184	0.181	0.19	0.239	0.24	RANDOM	21.467

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]
0.73		-0.22	-0.62		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.019
r_dihedral_angle_4_deg	13.436
r_dihedral_angle_3_deg	12.82
r_scangle_it	5.632
r_scbond_it	4.393
r_dihedral_angle_1_deg	4.37
r_mcangle_it	2.419
r_mcbond_it	1.626
r_angle_refined_deg	1.359
r_angle_other_deg	0.901
r_mcbond_other	0.628
r_symmetry_vdw_other	0.256
r_nbd_refined	0.203
r_nbd_other	0.193
r_nbtor_refined	0.185
r_symmetry_hbond_refined	0.177
r_xyhbond_nbd_refined	0.168
r_symmetry_vdw_refined	0.138
r_metal_ion_refined	0.091
r_nbtor_other	0.085
r_chiral_restr	0.082
r_xyhbond_nbd_other	0.027
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9225
Nucleic Acid Atoms
Solvent Atoms	985
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
autoSHARP	phasing