9P55 | pdb_00009p55

Structure of DNA-free long form XPD from Thermoplasma acidophilum

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	1M Sodium Potassium tartrate, 0.2M Sodium Chloride, 0.1M bis-Tris Propane pH 7

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.53	α = 90
b = 96	β = 90
c = 159.09	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	100	PIXEL	DECTRIS PILATUS3 6M		2024-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11583	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.11	159.09	99.1	0.16	0.999	11.2	12.8		52613

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.11	2.18	89.4		0.5405	0.091		9.8

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 (All)	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	2.127	12.822	51761	2530	99.401	0.204	0.202	0.2028	0.245	0.2452	RANDOM	69.538

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]
3.088			-2.102		-0.986

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.402
r_dihedral_angle_6_deg	15.289
r_lrange_it	11.458
r_lrange_other	11.451
r_dihedral_angle_2_deg	9.872
r_dihedral_angle_1_deg	8.577
r_scangle_other	8.525
r_scangle_it	8.519
r_mcangle_it	6.425
r_mcangle_other	6.424
r_scbond_other	5.457
r_scbond_it	5.453
r_mcbond_it	4.261
r_mcbond_other	4.261
r_angle_refined_deg	2.026
r_angle_other_deg	0.944
r_nbd_refined	0.168
r_nbtor_refined	0.151
r_symmetry_nbd_other	0.117
r_symmetry_nbd_refined	0.11
r_chiral_restr	0.108
r_xyhbond_nbd_refined	0.089
r_nbd_other	0.075
r_symmetry_nbtor_other	0.061
r_symmetry_xyhbond_nbd_refined	0.027
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5040
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing