2NWC | pdb_00002nwc

A 3.02 angstrom crystal structure of wild-type apo GroEL in a monoclinic space group

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KP8	PDB ENTRY 1kp8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	277	0.1 M imidazole, 35% MPD, 0.2 M MgCl2, pH 8.0, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.423	α = 90
b = 262.254	β = 99.83
c = 147.074	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	ADSC QUANTUM 315		2006-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.97	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.02	50	99.7	0.087	9.8	3.8	202060	202060

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)
	3.02	3.13	98.9		0.757	1.02	3.6	20078

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 1kp8	3.02	30	198054	188012	10042	99.72	0.22841	0.2266	0.27	0.26269	0.3	RANDOM	70.399

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]
-1.46		2.6	-3.3		5.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.52
r_dihedral_angle_3_deg	17.461
r_dihedral_angle_4_deg	14.941
r_dihedral_angle_1_deg	4.479
r_angle_refined_deg	0.971
r_scangle_it	0.733
r_scbond_it	0.411
r_mcangle_it	0.326
r_nbtor_refined	0.288
r_symmetry_vdw_refined	0.213

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.52
r_dihedral_angle_3_deg	17.461
r_dihedral_angle_4_deg	14.941
r_dihedral_angle_1_deg	4.479
r_angle_refined_deg	0.971
r_scangle_it	0.733
r_scbond_it	0.411
r_mcangle_it	0.326
r_nbtor_refined	0.288
r_symmetry_vdw_refined	0.213
r_symmetry_hbond_refined	0.195
r_mcbond_it	0.194
r_nbd_refined	0.184
r_xyhbond_nbd_refined	0.111
r_chiral_restr	0.066
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	53970
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
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.