4RGH | pdb_00004rgh

Human DNA Damage-Inducible Protein: From Protein Chemistry and 3D Structure to Deciphering its Cellular Role

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	292.15	0.2M amonium acetate, 0.1M Bis-Tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.87	α = 90
b = 86.4	β = 90
c = 52.12	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		CCD	MARMOSAIC 225 mm CCD		2010-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91573	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.9	87.09	87.2	0.09	9.5	4.6		21413

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	69.7		0.326	0.326	2.2	4.7	2460

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	26.44	20350	1042	87.32	0.2098	0.2076	0.22	0.2557	0.27	RANDOM	21.765

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]
0.23			2.27		-2.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.409
r_dihedral_angle_3_deg	14.624
r_dihedral_angle_4_deg	11.664
r_dihedral_angle_1_deg	6.806
r_angle_refined_deg	1.745
r_angle_other_deg	0.949
r_chiral_restr	0.097
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.409
r_dihedral_angle_3_deg	14.624
r_dihedral_angle_4_deg	11.664
r_dihedral_angle_1_deg	6.806
r_angle_refined_deg	1.745
r_angle_other_deg	0.949
r_chiral_restr	0.097
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1905
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	2

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.