Experiment: 5CL0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CCY	PDB entry 5CCY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	0.2 M magnesium chloride, 5 mM manganese chloride, 0.1 M Tris, pH 8.5, 30% w/v PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.946	α = 90
b = 73.946	β = 90
c = 128.584	γ = 120

Symmetry
Space Group	P 64 2 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		2014-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.000	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.22	50	99.8	0.098	0.094	0.027	8.3	14.1		10855

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.22	2.3	99.9		0.981	0.264	0.875		14	1053

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 5CCY	2.22	50	10308	522	99.9	0.1938	0.1915	0.2411	RANDOM	44.192

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]
-0.66	-0.33		-0.66		2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.406
r_dihedral_angle_4_deg	16.968
r_dihedral_angle_3_deg	14.256
r_dihedral_angle_1_deg	5.742
r_mcangle_it	2.726
r_mcbond_it	1.653
r_mcbond_other	1.651
r_angle_refined_deg	1.483
r_angle_other_deg	0.956
r_chiral_restr	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.406
r_dihedral_angle_4_deg	16.968
r_dihedral_angle_3_deg	14.256
r_dihedral_angle_1_deg	5.742
r_mcangle_it	2.726
r_mcbond_it	1.653
r_mcbond_other	1.651
r_angle_refined_deg	1.483
r_angle_other_deg	0.956
r_chiral_restr	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1458
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
SERGUI	data collection
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	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.