2QVP

CRYSTAL STRUCTURE OF A PUTATIVE METALLOPEPTIDASE (SAMA_0725) FROM SHEWANELLA AMAZONENSIS SB2B AT 2.00 A RESOLUTION

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	NANODROP, 1.6M (NH4)2SO4, 20.0% Glycerol, 0.1M Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.04	α = 90
b = 74.75	β = 95.19
c = 96.12	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)	2007-06-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97944	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	29.63	92.8	0.107	7.41	3.36		57061			20.14

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	2.07	99.5		0.518	1.87

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2	29.63	57042	2870	93.32	0.164	0.164	0.161	0.213	RANDOM	13.303

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]
-0.04		0.6	-0.03		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.959
r_dihedral_angle_4_deg	14.204
r_dihedral_angle_3_deg	12.754
r_scangle_it	7.131
r_scbond_it	5.365
r_dihedral_angle_1_deg	4.365
r_mcangle_it	2.903
r_mcbond_it	2.15
r_angle_refined_deg	1.863
r_angle_other_deg	1.394
r_mcbond_other	0.545
r_symmetry_hbond_refined	0.257
r_xyhbond_nbd_other	0.224
r_xyhbond_nbd_refined	0.191
r_symmetry_vdw_refined	0.183
r_nbd_refined	0.177
r_nbtor_refined	0.17
r_symmetry_vdw_other	0.165
r_nbd_other	0.154
r_chiral_restr	0.09
r_nbtor_other	0.088
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6159
Nucleic Acid Atoms
Solvent Atoms	526
Heterogen Atoms	122

Software

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