4QU6 | pdb_00004qu6

Crystal structure of a G-rich RNA sequence binding factor 1 (GRSF1) from Homo sapiens at 1.75 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DB1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M calcium chloride 20.0% polyethylene glycol 3350, 1 mM AGGGUG, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.48	α = 90
b = 60.48	β = 90
c = 59.38	γ = 90

Symmetry
Space Group	P 42 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	100	PIXEL	DECTRIS PILATUS 6M	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)	2013-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	1.75	42.766	98.7	0.105	17.73			11466		-3	22.802

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.8	88.1		0.014	1.451	1.6

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	2DB1	1.75	42.766	11465	546	98.58	0.1855	0.1826	0.19	0.2464	0.26	RANDOM	28.5744

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]
-1.19			-1.19		2.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.89
r_dihedral_angle_4_deg	13.984
r_dihedral_angle_3_deg	13.02
r_dihedral_angle_1_deg	5.946
r_mcangle_it	2.381
r_angle_refined_deg	1.548
r_mcbond_other	1.502
r_mcbond_it	1.501
r_angle_other_deg	0.846
r_chiral_restr	0.092

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.89
r_dihedral_angle_4_deg	13.984
r_dihedral_angle_3_deg	13.02
r_dihedral_angle_1_deg	5.946
r_mcangle_it	2.381
r_angle_refined_deg	1.548
r_mcbond_other	1.502
r_mcbond_it	1.501
r_angle_other_deg	0.846
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	805
Nucleic Acid Atoms	69
Solvent Atoms	85
Heterogen Atoms	12

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
MOLREP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.