5TEE | pdb_00005tee

Crystal structure of Gemin5 WD40 repeats in apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OW8	FFAS03/SCWRL models based on PDB entries 3ow8, 2hes, 3dm0
experimental model	PDB	2HES	FFAS03/SCWRL models based on PDB entries 3ow8, 2hes, 3dm0
experimental model	PDB	3DM0	FFAS03/SCWRL models based on PDB entries 3ow8, 2hes, 3dm0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	291	15% PEG4000, 0.2M ammonium acetate, 0.1M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.6	53.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.811	α = 90
b = 124.407	β = 119.49
c = 61.034	γ = 90

Symmetry
Space Group	P 1 21 1

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 315r		2011-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.65	48.71	98.9	0.091	0.107	0.054	0.997	10.8	3.8		93484

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	97.8		1.015	1.179	0.599	0.495	1.3	3.8	4501

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	FFAS03/SCWRL models based on PDB entries 3ow8, 2hes, 3dm0	1.65	48.47	88765	4684	98.76	0.165	0.1635	0.1753	0.1945	0.2055	21.435

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]
0.43		0.63	-0.6		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.549
r_dihedral_angle_4_deg	16.545
r_dihedral_angle_3_deg	11.664
r_dihedral_angle_1_deg	6.512
r_mcangle_it	3.331
r_mcbond_it	2.266
r_mcbond_other	2.244
r_angle_refined_deg	1.594
r_angle_other_deg	0.972
r_chiral_restr	0.1
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5298
Nucleic Acid Atoms
Solvent Atoms	420
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing
MOLREP	phasing