3FYA | pdb_00003fya

Crystal Structure of an R35A mutant of the Restriction-Modification Controller Protein C.Esp1396I

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CLC	PDB ENTRY 3CLC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	precipitation	8	277	150 mM NaCl, 40 mM Tris-HCl, 5 % w/v glycerol, 2.5 mM CaCl2, pH 8.0, precipitation, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.435	α = 90
b = 48.435	β = 90
c = 135.78	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 4		2008-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.9330	ESRF	ID14-2

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	2.952	41.959	100	0.263	0.263	1.394	7.6	3840	3839			86

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	2.95	3.11	100		0.412	0.412	1.9	5.5	553

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 3CLC	3	35.69	3615	164	100	0.249	0.248	0.25	0.267	0.28	RANDOM	56.744

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]
0.42	0.21		0.42		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.249
r_dihedral_angle_3_deg	24.613
r_dihedral_angle_4_deg	23.701
r_dihedral_angle_1_deg	5.971
r_angle_refined_deg	1.69
r_scangle_it	1.264
r_scbond_it	0.803
r_mcangle_it	0.623
r_symmetry_vdw_refined	0.409
r_mcbond_it	0.401

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.249
r_dihedral_angle_3_deg	24.613
r_dihedral_angle_4_deg	23.701
r_dihedral_angle_1_deg	5.971
r_angle_refined_deg	1.69
r_scangle_it	1.264
r_scbond_it	0.803
r_mcangle_it	0.623
r_symmetry_vdw_refined	0.409
r_mcbond_it	0.401
r_symmetry_hbond_refined	0.35
r_nbtor_refined	0.326
r_nbd_refined	0.261
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.126
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1208
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection

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.