Experiment: 4MKR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HFN	model generated by Robetta server with structure 4HFN as target

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	60 mM KCN, 28% PEG 2000 MME, 3 mM NaN3, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.93	α = 80.15
b = 76.34	β = 89.97
c = 93.45	γ = 85.66

Symmetry
Space Group	P 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	MARMOSAIC 225 mm CCD	Pt coated Si mirrors	2013-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

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	2.58	46.03	97.7	0.072	12.88	3.3	42573	42573		-3	49.681

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	2.58	2.65	86.3		0.539	2.19

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	model generated by Robetta server with structure 4HFN as target	2.58	46.03	42573	42573	2131	97.63	0.2309	0.2309	0.2281	0.2817	RANDOM	47.4358

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]
0.44	0.15	0.4	-0.36	0.75	0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.075
r_dihedral_angle_4_deg	21.788
r_dihedral_angle_3_deg	16.032
r_dihedral_angle_1_deg	6.411
r_angle_other_deg	3.771
r_mcangle_it	1.804
r_angle_refined_deg	1.674
r_mcbond_it	1.065
r_mcbond_other	1.065
r_chiral_restr	0.086

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.075
r_dihedral_angle_4_deg	21.788
r_dihedral_angle_3_deg	16.032
r_dihedral_angle_1_deg	6.411
r_angle_other_deg	3.771
r_mcangle_it	1.804
r_angle_refined_deg	1.674
r_mcbond_it	1.065
r_mcbond_other	1.065
r_chiral_restr	0.086
r_bond_refined_d	0.014
r_gen_planes_other	0.008
r_gen_planes_refined	0.006
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9119
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
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 R01GM133198.