6BCD | pdb_00006bcd

Crystal structure of Rev7-K44A/R124A/A135D in complex with Rev3-RBM2 (residues 1988-2014)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ABD	3ABD (excluding Rev3 peptide)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.25	289.15	well solution containing 100 mM sodium citrate, 1.6 M ammonium sulfate, pH=5.25 was mixed at 1:1 ratio with protein at 45 mg/mL in 5 mM HEPES, 100 mM NaCl, 10 mM DTT, pH=7.4

Crystal Properties
Matthews coefficient	Solvent content
2.7	53.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.58	α = 90
b = 64.58	β = 90
c = 116.547	γ = 120

Symmetry
Space Group	P 31 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	289.15	PIXEL	DECTRIS PILATUS3 S 6M		2016-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.976	CHESS	F1

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	1.43	116.55	98.5	0.045	0.048	0.016	41.78	9.6		51936

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	3ABD (excluding Rev3 peptide)	1.43	116.55	51936	2521	98.49	0.176	0.1749	0.18	0.1974	0.21	RANDOM	29.8026

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]
0.83	0.42		0.83		-2.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.145
r_dihedral_angle_4_deg	14.894
r_dihedral_angle_3_deg	14.726
r_dihedral_angle_1_deg	6.821
r_mcangle_it	4.69
r_angle_other_deg	3.679
r_mcbond_it	3.255
r_mcbond_other	3.255
r_angle_refined_deg	2.367
r_chiral_restr	0.148

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.145
r_dihedral_angle_4_deg	14.894
r_dihedral_angle_3_deg	14.726
r_dihedral_angle_1_deg	6.821
r_mcangle_it	4.69
r_angle_other_deg	3.679
r_mcbond_it	3.255
r_mcbond_other	3.255
r_angle_refined_deg	2.367
r_chiral_restr	0.148
r_gen_planes_other	0.027
r_bond_refined_d	0.026
r_gen_planes_refined	0.012
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1856
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement

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.