7YRP | pdb_00007yrp

Crystal structure of VIM-28 metallo-beta-lactamase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WHG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	289	1.4 M ammonium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.36	α = 90
b = 45.91	β = 103.59
c = 103.26	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS PILATUS 2M		2016-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-5A

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	67.73	99.66	0.102	8.3	3.1		43247

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	2.11			0.494	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2WHG	2	63.483	43245	2147	99.677	0.173	0.1718	0.18	0.2037	0.21	29.233

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]
-0.001		0.002	0.002		-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.509
r_dihedral_angle_3_deg	15.135
r_dihedral_angle_2_deg	9.11
r_dihedral_angle_1_deg	6.973
r_lrange_it	6.646
r_lrange_other	6.524
r_scangle_it	4.69
r_scangle_other	4.689
r_mcangle_it	3.144
r_mcangle_other	3.144
r_scbond_it	3.056
r_scbond_other	3.055
r_mcbond_it	2.206
r_mcbond_other	2.206
r_angle_refined_deg	1.39
r_angle_other_deg	0.968
r_symmetry_nbd_refined	0.394
r_nbd_refined	0.209
r_symmetry_nbd_other	0.203
r_nbd_other	0.175
r_symmetry_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.15
r_metal_ion_refined	0.083
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.066
r_bond_other_d	0.044
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3389
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing