Experiment: 3M51

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YZ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	277.15	0.1M CHES, 1.0M Na-Citrat, 30%(w/v) sucrose, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
4.13	70.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.44	α = 90
b = 97.44	β = 90
c = 214.27	γ = 90

Symmetry
Space Group	I 41 2 2

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	MARMOSAIC 225 mm CCD		2009-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00749	SLS	X10SA

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	3.25	48.74	99.9	0.061	22.39			8499		-3	85.969

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	3.25	3.5	99.9		0.47	4.6

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	1YZ5	3.25	48.74	8496	425	100	0.312	0.31	0.31	0.34	0.33	RANDOM	98.388

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]
-0.65			-0.65		1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.599
r_dihedral_angle_3_deg	14.548
r_dihedral_angle_4_deg	14.066
r_dihedral_angle_1_deg	3.485
r_angle_refined_deg	0.646
r_mcangle_it	0.44
r_scangle_it	0.325
r_mcbond_it	0.244
r_scbond_it	0.178
r_chiral_restr	0.043

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.599
r_dihedral_angle_3_deg	14.548
r_dihedral_angle_4_deg	14.066
r_dihedral_angle_1_deg	3.485
r_angle_refined_deg	0.646
r_mcangle_it	0.44
r_scangle_it	0.325
r_mcbond_it	0.244
r_scbond_it	0.178
r_chiral_restr	0.043
r_bond_refined_d	0.002
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2002
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	34

Software

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

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.