2HQX | pdb_00002hqx

Crystal structure of human P100 tudor domain conserved region

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MODIFIED MICROBATCH	7.9	291	1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (11.0 MG/ML) AND RESERVOIR SOLUTION CONTAINING 1.06M AMMONIUM SULFATE, 200.0 MM LITHIUM SULFATE, 0.1M TRIS PH 7.9, MODIFIED MICROBATCH, temperature 291K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.777	α = 90.03
b = 37.684	β = 105.32
c = 40.202	γ = 99.72

Symmetry
Space Group	P 1

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 300 mm CCD	ROSENBAUM	2005-12-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.9790	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.42	38.72	82.17	0.05	15.6	3.4	27043	25303		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.42	1.46	23.08		0.03		1.3	212

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	PT-SAS	THROUGHOUT	PDB ENTRY 2HQE	1.42	38.72	25303	25303	1348	82.17	0.23163	0.22947	0.23	0.27042	RANDOM	16.11

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]
0.33	-0.09	0.02	-0.18	-0.11	-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.932
r_dihedral_angle_4_deg	23.885
r_dihedral_angle_3_deg	13.104
r_dihedral_angle_1_deg	4.761
r_scangle_it	3.449
r_scbond_it	2.306
r_mcangle_it	1.348
r_angle_refined_deg	1.21
r_mcbond_it	0.81
r_xyhbond_nbd_refined	0.323
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.276
r_nbd_refined	0.245
r_symmetry_hbond_refined	0.197
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1378
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SCA2STRUCTURE	phasing