4JKB | pdb_00004jkb

Open and closed forms of V1788D human PRP8 RNase H-like domain with bound Mg 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
2.7	54.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.355	α = 90
b = 78.159	β = 90
c = 93.766	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		2013-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	0.97949	CLSI	08B1-1

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	1.3	50	99.4	0.041	13.3	5.5		135702	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	1.3	1.35	100		0.568		5.4	13514

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	1.3	40.04	123935	6249	90.53	0.1207	0.1194	0.1184	0.1453	0.1439	RANDOM	24.2539

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]
-0.24			-0.15		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.141
r_sphericity_free	31.477
r_dihedral_angle_4_deg	15.633
r_sphericity_bonded	14.405
r_dihedral_angle_3_deg	12.653
r_dihedral_angle_1_deg	5.788
r_rigid_bond_restr	2.84
r_angle_refined_deg	1.442
r_angle_other_deg	0.764
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3595
Nucleic Acid Atoms
Solvent Atoms	691
Heterogen Atoms	25

Software

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