Experiment: 5D2O

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, 2 mM manganese chloride, 0.1 M Tris, pH 8.5, 30% w/v PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.683	α = 90
b = 73.683	β = 90
c = 128.053	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	RAYONIX MX300-HS		2015-08-04	M	SINGLE WAVELENGTH

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

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	2.15	50	99.5	0.076	0.078	0.02	11.6	15.5		11735

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	2.15	2.23	98.7		0.732	0.761	0.206	0.878		13	1131

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	2.15	50	11060	638	99.37	0.1886	0.1851	0.2514	RANDOM	47.2

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]
-0.87	-0.43		-0.87		2.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.163
r_dihedral_angle_4_deg	19.592
r_dihedral_angle_3_deg	15.757
r_dihedral_angle_1_deg	7.018
r_mcangle_it	3.955
r_mcbond_other	2.714
r_mcbond_it	2.713
r_angle_refined_deg	2.303
r_angle_other_deg	1.177
r_chiral_restr	0.131

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.163
r_dihedral_angle_4_deg	19.592
r_dihedral_angle_3_deg	15.757
r_dihedral_angle_1_deg	7.018
r_mcangle_it	3.955
r_mcbond_other	2.714
r_mcbond_it	2.713
r_angle_refined_deg	2.303
r_angle_other_deg	1.177
r_chiral_restr	0.131
r_bond_refined_d	0.025
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1441
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	2

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	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.