Experiment: 5CLY

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	2.5M di-sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.017	α = 90
b = 85.929	β = 90
c = 63.964	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS PILATUS 6M-F		2014-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97242	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.23	63.964	97.5	0.042	0.049	0.024	13.5	3.8	67662	67662

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.23	1.3	94.1		0.725	0.725	0.417	1.1	3.8	9390

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	4PVL	1.23	35.7	64225	3409	97.18	0.1585	0.157	0.1857	RANDOM	25.514

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]
0.13			-0.01		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.172
r_sphericity_bonded	24.356
r_rigid_bond_restr	15.98
r_dihedral_angle_4_deg	14.817
r_dihedral_angle_3_deg	13.703
r_dihedral_angle_1_deg	6.403
r_mcangle_it	4.871
r_mcbond_it	4.763
r_mcbond_other	4.234
r_angle_other_deg	3.536

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.172
r_sphericity_bonded	24.356
r_rigid_bond_restr	15.98
r_dihedral_angle_4_deg	14.817
r_dihedral_angle_3_deg	13.703
r_dihedral_angle_1_deg	6.403
r_mcangle_it	4.871
r_mcbond_it	4.763
r_mcbond_other	4.234
r_angle_other_deg	3.536
r_angle_refined_deg	2.062
r_chiral_restr	0.134
r_bond_refined_d	0.023
r_gen_planes_other	0.02
r_gen_planes_refined	0.012
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1794
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
SCALA	data scaling
Coot	model building
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.