Experiment: 4ML5

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	277	1.6-2M magnesium chloride, 0.1M bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 184.23	α = 90
b = 184.23	β = 90
c = 184.23	γ = 90

Symmetry
Space Group	F 4 3 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	mirror	2012-10-08	M	SINGLE WAVELENGTH
2	1	x-ray		PIXEL	DECTRIS PILATUS 2M	mirror	2012-10-29	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.954	ESRF	BM14
2	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.751, 1.739	ELETTRA	5.2R

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	1.22	22.51	100	0.082	17.9	13.5	1071136	79449		2	8.162

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	1.22	1.29	100		0.375	5.1	8.6	11391

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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 3KA3	1.22	21.71	2	75437	75437	3987	99.96	0.13976	0.13904	0.15352	RANDOM	9.357

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.169
r_dihedral_angle_4_deg	18.699
r_sphericity_free	14.237
r_dihedral_angle_3_deg	13.492
r_sphericity_bonded	4.594
r_dihedral_angle_1_deg	4.546
r_rigid_bond_restr	4.202
r_angle_refined_deg	1.037
r_angle_other_deg	0.841
r_chiral_restr	0.058

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.169
r_dihedral_angle_4_deg	18.699
r_sphericity_free	14.237
r_dihedral_angle_3_deg	13.492
r_sphericity_bonded	4.594
r_dihedral_angle_1_deg	4.546
r_rigid_bond_restr	4.202
r_angle_refined_deg	1.037
r_angle_other_deg	0.841
r_chiral_restr	0.058
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1429
Nucleic Acid Atoms
Solvent Atoms	382
Heterogen Atoms	29

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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 R01GM133198.