4FLA | pdb_00004fla

Crystal structure of human RPRD1B, carboxy-terminal domain

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291	25% PEG-3350, 0.2M ammonium acetate, 0.1M HEPES, pH 7.5, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.221	α = 90
b = 100.221	β = 90
c = 142.887	γ = 90

Symmetry
Space Group	P 4 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 315		2012-02-24	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	MARMOSAIC 300 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97931	APS	19-ID
2	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97944	APS	23-ID-B

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	2.2	47.63	99.98	0.116	15.5351	9.62		37701

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	2.2	2.32	100		0.93		9.81	5387

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.2	40	37678	1587	99.867	0.233	0.2316	0.2575	0.2453	thin shells (sftools)	44.226

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]
1.791			1.791		-3.583

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.544
r_dihedral_angle_3_deg	14.351
r_dihedral_angle_4_deg	13.181
r_dihedral_angle_1_deg	4.173
r_angle_other_deg	1.326
r_angle_refined_deg	1.311
r_chiral_restr	0.066
r_bond_refined_d	0.013
r_bond_other_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3871
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	7

Software

Software
Software Name	Purpose
SCALA	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction