1SAX | pdb_00001sax

Three-dimensional structure of s.aureus methicillin-resistance regulating transcriptional repressor meci in complex with 25-bp ds-DNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OKR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	PEG 8000, magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.6	α = 90
b = 133.6	β = 90
c = 54.7	γ = 120

Symmetry
Space Group	P 31 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	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID13	0.9789	ESRF	ID13

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	39.7	97.8	0.089	19.7	3.5	14087	13777			86.5

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	93.6		0.5	2.3	2.9

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1OKR	2.8	39.7	13775	12877	898	97.81	0.21624	0.21624	0.21199	0.27601	RANDOM	31.56

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]
-2.1	-1.05		-2.1		3.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.512
r_scangle_it	2.539
r_angle_refined_deg	1.938
r_scbond_it	1.613
r_mcangle_it	1.488
r_mcbond_it	0.765
r_symmetry_vdw_refined	0.229
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.512
r_scangle_it	2.539
r_angle_refined_deg	1.938
r_scbond_it	1.613
r_mcangle_it	1.488
r_mcbond_it	0.765
r_symmetry_vdw_refined	0.229
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.097
r_bond_refined_d	0.014
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2032
Nucleic Acid Atoms	1019
Solvent Atoms	37
Heterogen Atoms	1

Software

Software
Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
AMoRE	phasing
REFMAC	refinement
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.