6LAE | pdb_00006lae

Crystal structure of the DNA-binding domain of human XPA in complex with DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6J44

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	289	20% PEG4000, 20% 2-propanol, 0.1 mM sodium citrate tribasic pH 5.6

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.112	α = 90
b = 69.112	β = 90
c = 63.938	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2017-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97775	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.8	50	93.2	0.104	0.119	0.056	10.2	4.1		7795			68.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	92.6		0.495	0.562	0.259		4.1

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6J44	2.81	43.7	7335	459	93.37	0.2198	0.2185	0.2369	0.2765	RANDOM	77.261

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]
18.6			18.6		-37.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.305
r_dihedral_angle_3_deg	15.818
r_dihedral_angle_4_deg	13.788
r_dihedral_angle_1_deg	7.409
r_angle_other_deg	2.316
r_angle_refined_deg	1.701
r_chiral_restr	0.094
r_bond_other_d	0.032
r_gen_planes_other	0.014
r_bond_refined_d	0.011
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1940
Nucleic Acid Atoms	450
Solvent Atoms	6
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing