4JK9 | pdb_00004jk9

Open and closed forms of wild-type human PRP8 RNase H-like domain with bound Co ion

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ENB	PDB entry 3ENB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	298	15% PEG 4000, 300mM MgCl2, 100mM Tris, pH 7.5, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.228	α = 90
b = 78.291	β = 90
c = 94.09	γ = 90

Symmetry
Space Group	P 21 21 21

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		2010-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

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	1.5	50	88.1	0.067	14.9	3.6		80130	1	1

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	1.5	1.55	96.3		0.447		2.8	8619

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 3ENB	1.5	34.27	80075	4216	88.01	0.1661	0.1639	0.16	0.2049	0.2	RANDOM	22.4173

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]
-0.59			0.41		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.098
r_dihedral_angle_4_deg	16.987
r_dihedral_angle_3_deg	13.447
r_sphericity_free	11.068
r_dihedral_angle_1_deg	5.866
r_scangle_it	5.308
r_sphericity_bonded	4.693
r_scbond_it	4.084
r_mcangle_it	2.915
r_mcbond_it	2.466
r_rigid_bond_restr	2.045
r_angle_refined_deg	1.814
r_mcbond_other	0.93
r_angle_other_deg	0.885
r_symmetry_vdw_other	0.248
r_nbd_refined	0.235
r_xyhbond_nbd_refined	0.214
r_symmetry_vdw_refined	0.209
r_nbd_other	0.186
r_nbtor_refined	0.182
r_symmetry_hbond_refined	0.16
r_chiral_restr	0.118
r_metal_ion_refined	0.091
r_nbtor_other	0.086
r_bond_refined_d	0.022
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3575
Nucleic Acid Atoms
Solvent Atoms	518
Heterogen Atoms	15

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CLS	data collection
DENZO	data reduction
REFMAC	phasing