5Q4D | pdb_00005q4d

PanDDA analysis group deposition -- Crystal Structure of DCLRE1A after initial refinement with no ligand modelled (structure 78)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	30% PEG 1000, 0.1M MIB buffer

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.84	α = 90
b = 58.03	β = 90
c = 114.41	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		PIXEL	DECTRIS PILATUS 6M		2016-09-29		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.8	29.01	99.9	0.185	0.202	0.08	0.995	9.3	6.4		32780

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	1.8	1.85	100		1.78	1.935	0.75	0.521		6.5	2401

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	5aho	1.8	29.01	31099	1623	99.87	0.2222	0.2195	0.23	0.2771	0.28	RANDOM	32.771

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]
-2.36			3.25		-0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.005
r_dihedral_angle_4_deg	15.414
r_dihedral_angle_3_deg	13.437
r_dihedral_angle_1_deg	7.084
r_mcangle_it	4.664
r_mcbond_it	3.08
r_mcbond_other	3.076
r_angle_refined_deg	1.766
r_angle_other_deg	1.051
r_chiral_restr	0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.005
r_dihedral_angle_4_deg	15.414
r_dihedral_angle_3_deg	13.437
r_dihedral_angle_1_deg	7.084
r_mcangle_it	4.664
r_mcbond_it	3.08
r_mcbond_other	3.076
r_angle_refined_deg	1.766
r_angle_other_deg	1.051
r_chiral_restr	0.108
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2692
Nucleic Acid Atoms
Solvent Atoms	310
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	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.