2WYQ | pdb_00002wyq

THE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE (UBL) DOMAIN OF HHR23A (HUMAN HOMOLOGUE A OF RAD23)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		0.1 M HEPES PH 7.5, 2% PEG 400 AND 2.0 M AMMONIUM SULFATE, AT ROOM TEMPERATURE

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.434	α = 90
b = 78.434	β = 90
c = 63.472	γ = 120

Symmetry
Space Group	P 65 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	ADSC CCD		2009-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

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	1.65	63.57	100	0.08	5.86	36.17		14363		2	21.4

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	1.65	1.74	100		0.35	2.08	23

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 2BWF	1.651	35	14330	706	99.902	0.126	0.1241	0.2	0.1598	0.24	RANDOM	9.296

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]
0.026	0.013		0.026		-0.039

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.598
r_dihedral_angle_4_deg	22.156
r_sphericity_free	20.126
r_dihedral_angle_3_deg	14.992
r_scangle_it	7.41
r_dihedral_angle_1_deg	6.351
r_sphericity_bonded	5.566
r_scbond_it	5.423
r_mcangle_it	3.553
r_angle_other_deg	3.113
r_mcbond_it	2.576
r_rigid_bond_restr	2.479
r_angle_refined_deg	2.288
r_mcbond_other	1.171
r_nbd_refined	0.299
r_chiral_restr	0.276
r_symmetry_hbond_refined	0.273
r_xyhbond_nbd_refined	0.269
r_symmetry_vdw_refined	0.218
r_nbd_other	0.189
r_nbtor_refined	0.168
r_symmetry_vdw_other	0.147
r_nbtor_other	0.095
r_bond_refined_d	0.029
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	603
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing