3C5A | pdb_00003c5a

Crystal structure of the C-terminal deleted mutant of the class A carbapenemase KPC-2 at 1.23 angstrom

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	291	20% PEG4K, 0.1M KSCN, 0.1M Citrate, VAPOR DIFFUSION, SITTING DROP, pH4.0, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.89	α = 90
b = 65.99	β = 90
c = 72.13	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	ADSC QUANTUM 315	mirror 1, double crystal, mirror 2	2007-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.979	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.23	27.17	97.7	22.55	13.6		65197			14.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.23	1.31	91.9		0.196	6.5	11.6	9747

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 (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	PDB ENTRY 2ODS	1.23	27.17	65188	3259	100	0.182	0.181	0.16	0.196	0.18	RANDOM	11.796

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]
0.1			-0.01		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.311
r_dihedral_angle_3_deg	11.727
r_dihedral_angle_4_deg	9.134
r_dihedral_angle_1_deg	5.739
r_scangle_it	2.07
r_scbond_it	1.398
r_angle_refined_deg	1.139
r_mcangle_it	0.933
r_mcbond_it	0.558
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.311
r_dihedral_angle_3_deg	11.727
r_dihedral_angle_4_deg	9.134
r_dihedral_angle_1_deg	5.739
r_scangle_it	2.07
r_scbond_it	1.398
r_angle_refined_deg	1.139
r_mcangle_it	0.933
r_mcbond_it	0.558
r_nbtor_refined	0.304
r_xyhbond_nbd_refined	0.257
r_nbd_refined	0.217
r_symmetry_vdw_refined	0.198
r_chiral_restr	0.072
r_symmetry_hbond_refined	0.067
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1972
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	13

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Xnemo	data collection
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.