Experiment: 4MXA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4M97	PDB ENTRY 4M97

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	protein solution: 25 mM HEPES pH 7.0, 0.5 M NaCl, 5% glycerol, 5 mM DTT, 20 mM EGTA, 3mg/ml protein, 0.2 mM RM-1-132, 1% DMSO; crystallization buffer: 30% PEG 3350, 0.2 M ammonium citrate, 0.1 M BisTris pH 5.3, 5 mM DTT, vapor diffusion, sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.22	α = 90
b = 72.53	β = 99.28
c = 65.65	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M		2013-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97939	SSRL	BL12-2

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	47.59	89.1	0.376	3.6	2.8		8027

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	3.21	89.7		0.018	1	2.7	1432

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 4M97	3	47.63	7097	328	78.52	0.2538	0.2526	0.2793	RANDOM	73.6112

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]
-2.98		0.4	0.97		1.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.389
r_dihedral_angle_3_deg	16.412
r_dihedral_angle_4_deg	15.291
r_dihedral_angle_1_deg	5.533
r_mcangle_it	2.602
r_mcbond_it	1.509
r_mcbond_other	1.507
r_angle_refined_deg	1.43
r_angle_other_deg	0.801
r_chiral_restr	0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.389
r_dihedral_angle_3_deg	16.412
r_dihedral_angle_4_deg	15.291
r_dihedral_angle_1_deg	5.533
r_mcangle_it	2.602
r_mcbond_it	1.509
r_mcbond_other	1.507
r_angle_refined_deg	1.43
r_angle_other_deg	0.801
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3670
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	30

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	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.