2RHB | pdb_00002rhb

Crystal structure of Nsp15-H234A mutant- Hexamer in asymmetric unit

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2H85

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.9	289	at 10-15 mg/ml of protein in 0.05-0.1 M MgCl2, 3-5 % MPD and 0.1 M tri-sodium citrate dehydrate (pH 5.6-5.9). , VAPOR DIFFUSION, HANGING DROP, temperature 289K, pH 5.90

Crystal Properties
Matthews coefficient	Solvent content
3.37	63.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 305.757	α = 90
b = 305.757	β = 90
c = 88.74	γ = 120

Symmetry
Space Group	H 3

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	MAR CCD 165 mm		2004-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B		APS	14-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	152.5	91.9				66521

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.8	2.87	78.2

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	2H85	2.8	50	66521	66521	3507	91.96	0.20043	0.19788	0.21	0.25953	0.26	RANDOM	60.345

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]
0.58	0.29		0.58		-0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.533
r_dihedral_angle_4_deg	19.552
r_dihedral_angle_3_deg	18.466
r_dihedral_angle_1_deg	5.816
r_scangle_it	2.122
r_scbond_it	1.334
r_mcangle_it	1.257
r_angle_refined_deg	1.067
r_mcbond_it	0.677
r_nbtor_refined	0.301
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.155
r_xyhbond_nbd_refined	0.126
r_symmetry_hbond_refined	0.107
r_chiral_restr	0.075
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
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	16071
Nucleic Acid Atoms
Solvent Atoms	441
Heterogen Atoms

Software

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