1X8I | pdb_00001x8i

Crystal Structure of the Zinc Carbapenemase CphA in Complex with the Antibiotic Biapenem

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X8H	CphA (N220G) mutant

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	280	PEG, AS, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K

Crystal Properties
Matthews coefficient	Solvent content
2.5	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.836	α = 90
b = 101.513	β = 90
c = 117.364	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH		2003-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE

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	1.9	26.5	93.1	0.12	0.12	3.7	5.9		20636

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	1.9	1.96	99.9		0.29	0.29	2.1	5.2

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	CphA (N220G) mutant	1.9	26.5	19554	1051	99.94	0.153	0.15311	0.15147	0.16	0.18308	0.19	RANDOM	16.545

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]
0.35			-0.28		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.378
r_sphericity_bonded	4.489
r_scangle_it	4.224
r_sphericity_free	3.806
r_scbond_it	2.574
r_angle_refined_deg	1.748
r_mcangle_it	1.461
r_angle_other_deg	0.95
r_mcbond_it	0.815
r_symmetry_vdw_other	0.376
r_nbd_refined	0.375
r_nbd_other	0.246
r_symmetry_vdw_refined	0.215
r_xyhbond_nbd_refined	0.181
r_symmetry_hbond_refined	0.164
r_chiral_restr	0.098
r_nbtor_other	0.083
r_bond_refined_d	0.017
r_gen_planes_other	0.016
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1754
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	62

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CCP4	model building
REFMAC	refinement
CCP4	data scaling
CCP4	phasing