2RB7 | pdb_00002rb7

Crystal structure of co-catalytic metallopeptidase (YP_387682.1) from Desulfovibrio desulfuricans G20 at 1.60 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.1	277	NANODROP, 0.2M Sodium fluoride, 20.0% PEG 3350, No Buffer pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.85	α = 90
b = 82.19	β = 91.37
c = 89.34	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)	2007-06-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97901, 0.97926	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	1.6	27.995	98.7	0.045	9.92	3.28		101945		-3	18.5

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	1.6	1.66	94.5		0.314	2.2

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	1.6	27.995	101918	5090	99.4	0.155	0.154	0.16	0.18	0.19	RANDOM	14.803

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]
0.46		-0.75	0.17		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.953
r_dihedral_angle_4_deg	19.97
r_dihedral_angle_3_deg	12.784
r_scangle_it	6.736
r_dihedral_angle_1_deg	5.614
r_scbond_it	4.746
r_mcangle_it	2.642
r_mcbond_it	2.199
r_angle_refined_deg	1.624
r_angle_other_deg	1.007
r_mcbond_other	0.548
r_symmetry_vdw_other	0.256
r_nbd_refined	0.224
r_nbd_other	0.21
r_symmetry_hbond_refined	0.197
r_symmetry_vdw_refined	0.179
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.164
r_xyhbond_nbd_other	0.117
r_chiral_restr	0.103
r_nbtor_other	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5505
Nucleic Acid Atoms
Solvent Atoms	916
Heterogen Atoms	51

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