Experiment: 5DQM

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	2	293	0.1 M Citric acid pH 5.5, 1 M LiCl, 30 % PEG 6000. Prior to data collection pH of the cryoprotectant was adjusted to 2.0 by citric acid

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.268	α = 90
b = 51.528	β = 97.7
c = 47.529	γ = 90

Symmetry
Space Group	P 1 21 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		2015-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

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	1.3	30	96.4	0.048	9.6	3.8		53938

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	1.3	1.35	93.6		0.582		3.6	5207

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	5DQB	1.3	22.28	52764	1093	96.15	0.1632	0.1622	0.2082	RANDOM	17.335

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]
-0.03		-0.04	0.07		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.34
r_sphericity_free	16.983
r_sphericity_bonded	14.469
r_dihedral_angle_4_deg	14.161
r_dihedral_angle_3_deg	14.063
r_rigid_bond_restr	11.657
r_dihedral_angle_1_deg	7.807
r_angle_refined_deg	2.505
r_angle_other_deg	1.191
r_chiral_restr	0.181

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.34
r_sphericity_free	16.983
r_sphericity_bonded	14.469
r_dihedral_angle_4_deg	14.161
r_dihedral_angle_3_deg	14.063
r_rigid_bond_restr	11.657
r_dihedral_angle_1_deg	7.807
r_angle_refined_deg	2.505
r_angle_other_deg	1.191
r_chiral_restr	0.181
r_bond_refined_d	0.028
r_gen_planes_refined	0.013
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1812
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	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 R01GM133198.