3AL3 | pdb_00003al3

Crystal Structure of TopBP1 BRCT7/8-BACH1 peptide complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AL2	PDB ENTRY 3AL2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	Sodium formate, pH 8, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.069	α = 90
b = 78.069	β = 90
c = 136.766	γ = 120

Symmetry
Space Group	P 62 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	MARMOSAIC 225 mm CCD		2010-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1		CLSI	08ID-1

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	2.15	50	99.9	0.06	28.987	6.8		14063

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	2.15	2.23	100		0.526		6.2	1365

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 3AL2	2.15	33.9	14021	699	99.86	0.1975	0.1955	0.1947	0.2364	0.2403	RANDOM	47.2525

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]
0.27	0.14		0.27		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.499
r_dihedral_angle_4_deg	25.874
r_dihedral_angle_3_deg	17.275
r_dihedral_angle_1_deg	5.822
r_scangle_it	2.459
r_scbond_it	1.501
r_angle_refined_deg	1.258
r_mcangle_it	1.053
r_mcbond_it	0.572
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1823
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	3

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
HKL-2000	data scaling