3CLC | pdb_00003clc

Crystal Structure of the Restriction-Modification Controller Protein C.Esp1396I Tetramer in Complex with its Natural 35 Base-Pair Operator

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	289	50 mM MES, 40 mM MgCl2, 25% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.68	66.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.48	α = 90
b = 104.48	β = 90
c = 139.29	γ = 120

Symmetry
Space Group	P 65

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		2007-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9322	ESRF	ID29

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	2.8	20	98.5	0.043	33.66		21194	21198			63.204

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	2.8	2.9	98.5		0.393	4.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.8	19.06	21157	1086	99.81	0.209	0.207	0.21	0.239	0.24	RANDOM	94.261

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]
-0.23	-0.11		-0.23		0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.065
r_dihedral_angle_3_deg	24.805
r_dihedral_angle_4_deg	17.41
r_dihedral_angle_1_deg	8.556
r_scangle_it	3.388
r_scbond_it	2.159
r_mcangle_it	1.689
r_angle_refined_deg	1.328
r_mcbond_it	1.117
r_symmetry_vdw_refined	0.341

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.065
r_dihedral_angle_3_deg	24.805
r_dihedral_angle_4_deg	17.41
r_dihedral_angle_1_deg	8.556
r_scangle_it	3.388
r_scbond_it	2.159
r_mcangle_it	1.689
r_angle_refined_deg	1.328
r_mcbond_it	1.117
r_symmetry_vdw_refined	0.341
r_nbtor_refined	0.338
r_nbd_refined	0.295
r_xyhbond_nbd_refined	0.243
r_chiral_restr	0.093
r_symmetry_hbond_refined	0.034
r_gen_planes_refined	0.011
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2496
Nucleic Acid Atoms	1429
Solvent Atoms	4
Heterogen Atoms	2

Software

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

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.