4YUD | pdb_00004yud

Crystal structure of a RNA binding motif protein 39 (RBM39) from Homo sapiens at 1.28 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CQ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% polyethylene glycol 3350, 0.20M sodium fluoride, 1mM RNA-6b UAAUAA

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.574	α = 90
b = 26.711	β = 90
c = 35.015	γ = 90

Symmetry
Space Group	P 21 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)	2013-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	1.0	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.28	32.461	92.2	0.023	0.027	0.013	27.7	3.9	20012	20012

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.28	1.35	63		0.285	0.285	0.355	0.205	2.7	2.3	1948

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	2CQ4	1.28	32.461	19974	1038	92.11	0.1487	0.1463	0.15	0.1942	0.19	RANDOM	21.6503

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]
-0.54			-0.89		1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.951
r_dihedral_angle_4_deg	16.028
r_dihedral_angle_3_deg	10.413
r_sphericity_free	8.26
r_scangle_it	6.737
r_scbond_it	4.776
r_dihedral_angle_1_deg	4.455
r_mcangle_it	4.45
r_sphericity_bonded	4.145
r_mcbond_it	2.968
r_rigid_bond_restr	2.005
r_angle_refined_deg	1.698
r_mcbond_other	1.595
r_angle_other_deg	0.887
r_chiral_restr	0.096
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	666
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms

Software

Software
Software Name	Purpose
PDB_EXTRACT	data extraction
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SCALA	data scaling