1YDX | pdb_00001ydx

Crystal structure of Type-I restriction-modification system S subunit from M. genitalium

X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.601	α = 90
b = 76.601	β = 90
c = 174.847	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						M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97935, 0.97950, 0.97565, 0.97930	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	2.2	38	99.6	0.083	16.7	7	30905	30905

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	2.2	2.32	98.8		0.62	2.5	6.2	4409

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.3	20	29276	25685	1385	99.76	0.1988	0.1988	0.19699	0.1945	0.23126	0.2282	RANDOM	40.815

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]
1.55	-0.77		1.55		-2.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.326
r_dihedral_angle_3_deg	18.046
r_dihedral_angle_4_deg	13.005
r_dihedral_angle_1_deg	6.337
r_scangle_it	3.413
r_scbond_it	2.292
r_angle_refined_deg	1.541
r_mcangle_it	1.279
r_mcbond_it	0.817
r_nbtor_refined	0.301

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3032
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement

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.