2FZS | pdb_00002fzs

Crystal structure of E. coli ClpP with a Peptide Chloromethyl Ketone Covalently Bound at the Active Site

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	0.1M tri-sodium citrate, 0.15M ammonium acetate, 30% PEG 4000 , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 190.7	α = 90
b = 101	β = 99
c = 155.4	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	CCD	ADSC QUANTUM 4	mirrors	2004-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9B	1.2547	NSLS	X9B

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	1.9	50	94	0.051	21.5	3.5		215884

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	1.9	1.97	95.1		0.373	2.8	1.7

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 (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	PDB ENTRY: 1TYF	1.9	15	203390	203390	10731	93.8	0.176	0.176	0.173	0.17	0.233	0.23	RANDOM	36

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]
0.85		0.51	0.28		-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.968
r_dihedral_angle_4_deg	19.434
r_dihedral_angle_3_deg	17.177
r_dihedral_angle_1_deg	6.082
r_scangle_it	4.176
r_scbond_it	2.766
r_angle_refined_deg	1.787
r_mcangle_it	1.537
r_mcbond_it	1.046
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.968
r_dihedral_angle_4_deg	19.434
r_dihedral_angle_3_deg	17.177
r_dihedral_angle_1_deg	6.082
r_scangle_it	4.176
r_scbond_it	2.766
r_angle_refined_deg	1.787
r_mcangle_it	1.537
r_mcbond_it	1.046
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.237
r_nbd_refined	0.223
r_symmetry_hbond_refined	0.2
r_xyhbond_nbd_refined	0.172
r_chiral_restr	0.126
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20264
Nucleic Acid Atoms
Solvent Atoms	2855
Heterogen Atoms	650

Software

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