5TF2 | pdb_00005tf2

CRYSTAL STRUCTURE OF THE WD40 DOMAIN OF THE HUMAN PROLACTIN REGULATORY ELEMENT-BINDING PROTEIN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ERJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	PREB protein was mixed with elastase at 1:1000 (w/w) ratio before setting up crystallization. Crystals were grown at 293 K using the sitting drop method by mixing 0.5 uL protein with 0.5 uL well solution consisting of 1.4M Malonate, pH 7.0. The crystals were cryoprotected by immersion in Paratone.

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.708	α = 90
b = 160.708	β = 90
c = 83.014	γ = 120

Symmetry
Space Group	P 64 2 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	CCD	ADSC QUANTUM 315		2014-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.92045	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.8	50	100	0.107	0.111	0.031	6.3	12.4		16070

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	100		0.779	0.898		12.7

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	1ERJ	2.8	50	15265	784	99.93	0.19	0.1888	0.19	0.214	0.22	RANDOM	46.35

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]
0.51	0.25		0.51		-1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.632
r_dihedral_angle_4_deg	17.866
r_dihedral_angle_3_deg	13.107
r_dihedral_angle_1_deg	6.614
r_mcangle_it	1.482
r_angle_refined_deg	1.305
r_angle_other_deg	0.849
r_mcbond_it	0.804
r_mcbond_other	0.802
r_chiral_restr	0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.632
r_dihedral_angle_4_deg	17.866
r_dihedral_angle_3_deg	13.107
r_dihedral_angle_1_deg	6.614
r_mcangle_it	1.482
r_angle_refined_deg	1.305
r_angle_other_deg	0.849
r_mcbond_it	0.804
r_mcbond_other	0.802
r_chiral_restr	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2519
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	1

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
BALBES	phasing
BUCCANEER	model building

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.