5Y38 | pdb_00005y38

Crystal structure of C7orf59-HBXIP complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MS6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	289	0.16 M ammonium sulfate, 0.08 M sodium acetate trihydrate (pH 4.6), and 20% (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.541	α = 90
b = 58.541	β = 90
c = 90.012	γ = 120

Symmetry
Space Group	P 32 2 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	RAYONIX MX225HE		2015-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	1.0000	SSRF	BL17U1

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	2.8	50	97.1	0.095	9.3	6.3		4579

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	2.8	2.9	98		0.477		5.7

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3MS6	2.8	50	4370	207	97.38	0.2168	0.215	0.2563	0.2278	RANDOM	50.674

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]
-1.55	-0.77		-1.55		2.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.369
r_dihedral_angle_3_deg	20.271
r_dihedral_angle_4_deg	12.664
r_sphericity_free	11.466
r_rigid_bond_restr	6.794
r_dihedral_angle_1_deg	5.239
r_sphericity_bonded	5.083
r_angle_refined_deg	1.075
r_chiral_restr	0.302
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1205
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	15

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction