3E0C | pdb_00003e0c

Crystal Structure of DNA Damage-Binding protein 1(DDB1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B5M	PDB entry 2B5M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1 M Bis tris, pH 6.5,0.2 M Lithium sulfate, 25% PEG 3350, 1:6000 Protein:Chymotrypsin , VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.607	α = 90
b = 124.153	β = 90
c = 167.822	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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97935	APS	19-ID

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	2.4	50	100	0.091		7.3		51628

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)
	2.4	2.44	100		0.903		7.3	2523

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2B5M	2.41	49.88	51552	2623	99.7	0.227	0.224	0.2379	0.283	0.2899	RANDOM	24.249

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]
-0.68			1.52		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.595
r_dihedral_angle_4_deg	19.551
r_dihedral_angle_3_deg	15.222
r_dihedral_angle_1_deg	7.926
r_scangle_it	2.856
r_scbond_it	1.861
r_angle_refined_deg	1.517
r_mcangle_it	1.335
r_mcbond_it	0.764
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.217
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.183
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.094
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7545
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction