2FAZ | pdb_00002faz

Ubiquitin-Like Domain of Human Nuclear Zinc Finger Protein NP95

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SIF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	Well Solution: 20.0% P3350, 0.2 M tri-Li Citrate; Protein Buffer: 20 mM Tris pH 8.0, 100 mM NaCl, 5 mM beta- mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.554	α = 90
b = 89.554	β = 90
c = 108.279	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	SBC-3		2005-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97868	APS	19-BM

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	22.8	98.5	0.056	28.67	5.1	17642	17642		-3

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	2.07	99		0.626	2.36	5.2	1728

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1SIF	2	22.8	17642	16778	903	98.75	0.21959	0.2179	0.2209	0.25243	0.2506	RANDOM	36.319

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]
2.39	1.2		2.39		-3.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.643
r_dihedral_angle_4_deg	22.912
r_dihedral_angle_3_deg	18.002
r_dihedral_angle_1_deg	6.356
r_scangle_it	5.914
r_scbond_it	4.148
r_mcangle_it	2.569
r_mcbond_it	1.946
r_angle_refined_deg	1.736
r_nbtor_refined	0.315
r_nbd_refined	0.232
r_symmetry_vdw_refined	0.211
r_symmetry_hbond_refined	0.185
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.117
r_bond_refined_d	0.018
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1273
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms

Software

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