6BI7 | pdb_00006bi7

Crystal structure of Rev7-WT/Rev3 as a monomer under high-salt conditions

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6BC8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289.15	hRev7/3 at 60 mg/mL in 5 mM HEPES, 100 mM NaCl, 10 mM DTT, pH=7.4 was mixed in a 1:1 ratio with a well solution consisting of 100 mM sodium citrate, 1M LiCl, 7.5% (w/v) PEG6000 at pH=4.75. Crystals were frozen in the reservoir solution with the addition of 20% (w/v) sucrose

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.696	α = 90
b = 89.696	β = 90
c = 284.841	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	77	PIXEL	DECTRIS PILATUS3 S 6M		2016-03-03	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)	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	284.84	99.8	0.044	21.1	9.6		33727

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.85	99.9		0.168	0.946	2.2	9.5

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	6BC8	2.8	284.84	33727	1715	99.75	0.2778	0.2754	0.27	0.3213	0.32	RANDOM	94.6819

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]
-3.5	-1.75		-3.5		11.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.701
r_dihedral_angle_4_deg	22.302
r_dihedral_angle_3_deg	17.212
r_mcangle_it	11.895
r_mcbond_it	7.657
r_mcbond_other	7.656
r_dihedral_angle_1_deg	7.617
r_angle_other_deg	3.518
r_angle_refined_deg	1.527
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6426
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
Coot	model building