2ZKG | pdb_00002zkg

Crystal structure of unliganded SRA domain of mouse Np95

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BI7	PDB ENTRY 3BI7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	0.1M Tris-HCl (pH8.0), 0.1M Sodium acetate, 12% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.334	α = 91.11
b = 67.013	β = 65.01
c = 69.572	γ = 84.48

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	ADSC QUANTUM 315		2008-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

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	1.77	50	95.4	0.071		3.8		96644			23.02

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	1.77	1.83	77.3		0.372		2.8

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 3BI7	1.77	29.31	91798	4845	95.24	0.18797	0.18648	0.19	0.21678	0.22	RANDOM	25.491

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]
-0.6	0.45	0.83	-0.27	0.46	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.55
r_dihedral_angle_4_deg	18.123
r_dihedral_angle_3_deg	12.704
r_dihedral_angle_1_deg	5.971
r_scangle_it	3.293
r_scbond_it	2.296
r_angle_refined_deg	1.401
r_mcangle_it	1.389
r_mcbond_it	1.233
r_angle_other_deg	0.995
r_symmetry_vdw_other	0.276
r_symmetry_vdw_refined	0.231
r_mcbond_other	0.227
r_nbd_other	0.216
r_nbd_refined	0.196
r_nbtor_refined	0.183
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.105
r_nbtor_other	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5917
Nucleic Acid Atoms
Solvent Atoms	514
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing