3CT9 | pdb_00003ct9

Crystal structure of a putative zinc peptidase (NP_812461.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.31 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	277	NANODROP, 0.2M NH4I, 20.0% PEG 3350, No Buffer pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.34	α = 90
b = 67.25	β = 94.28
c = 107.89	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 mirror (vertical focusing)	2007-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97910	SSRL	BL11-1

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	2.28	28.513	93.7	0.043	12.23			31807		-3	39.305

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	2.28	2.36	42.6		0.24	3

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	SAD	THROUGHOUT	2.31	28.513	31794	1613	98.43	0.197	0.194	0.2	0.253	0.26	RANDOM	29.051

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]
-1.27		0.79	0.31		1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.636
r_dihedral_angle_4_deg	15.622
r_dihedral_angle_3_deg	13.105
r_dihedral_angle_1_deg	3.898
r_angle_refined_deg	1.732
r_scangle_it	1.511
r_mcangle_it	1.448
r_angle_other_deg	1.03
r_scbond_it	1.03
r_mcbond_it	0.96
r_symmetry_vdw_refined	0.3
r_symmetry_vdw_other	0.258
r_mcbond_other	0.229
r_nbd_refined	0.202
r_symmetry_hbond_refined	0.198
r_nbd_other	0.187
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.168
r_chiral_restr	0.107
r_nbtor_other	0.088
r_bond_refined_d	0.016
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	5230
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	41

Software

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