2GKL

Crystal structure of the zinc carbapenemase CPHA in complex with the inhibitor pyridine-2,4-dicarboxylate

X-RAY DIFFRACTION

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Starting Model(s)

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

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 = 42.638	α = 90
b = 101.211	β = 90
c = 117.121	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		2005-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591	1.54179

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	1.86	50	99.4	0.07	0.07	7.4	6.4	21756	21647	2	2

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	1.86	1.91	97.3		0.179	0.179	4.1	6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1X8H	1.86	21.9	2	21625	20495	1102	99.29	0.161	0.16084	0.15898	0.19617	RANDOM	14.148

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]
-0.21			0.48		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.922
r_dihedral_angle_4_deg	20.365
r_dihedral_angle_3_deg	14.122
r_dihedral_angle_1_deg	6.18
r_scangle_it	3.474
r_scbond_it	2.185
r_angle_refined_deg	1.365
r_angle_other_deg	1.218
r_mcangle_it	1.181
r_mcbond_it	0.758
r_nbd_refined	0.359
r_symmetry_vdw_other	0.263
r_nbd_other	0.205
r_mcbond_other	0.205
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.157
r_symmetry_hbond_refined	0.106
r_symmetry_vdw_refined	0.104
r_nbtor_other	0.088
r_chiral_restr	0.082
r_bond_refined_d	0.013
r_bond_other_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1758
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	31

Software

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