Experiment: 6MXS

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BDY	PDB entry 3BDY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.6	295	0.1 M tri-sodium citrate, pH 5.6, 12% PEG4000, 10% isopropanol

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.679	α = 90
b = 95.96	β = 103.68
c = 110.11	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	CCD	RAYONIX MX-300		2017-01-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9795	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.95	50	99.1	0.223	0.261	0.134	0.947	26.6	3.7		95751

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	98.4		0.893	1.042	0.533	0.537		3.8

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3BDY	1.95	50	90638	4831	98.71	0.1932	0.1913	0.2288	RANDOM	29.286

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]
2.54		-0.78	-0.94		-1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.057
r_dihedral_angle_4_deg	18.81
r_dihedral_angle_3_deg	15.064
r_dihedral_angle_1_deg	7.536
r_angle_refined_deg	1.88
r_angle_other_deg	0.882
r_chiral_restr	0.115
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.057
r_dihedral_angle_4_deg	18.81
r_dihedral_angle_3_deg	15.064
r_dihedral_angle_1_deg	7.536
r_angle_refined_deg	1.88
r_angle_other_deg	0.882
r_chiral_restr	0.115
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6649
Nucleic Acid Atoms
Solvent Atoms	844
Heterogen Atoms	11

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

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.