6WZZ | pdb_00006wzz

GID4 in complex with VGLWKS peptide

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	0.03 M Citric acid, pH 7.6 and 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.781	α = 90
b = 40.648	β = 98.102
c = 56.319	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	PIXEL	DECTRIS PILATUS 6M		2018-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97625	CLSI	08ID-1

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	1.6	40.65	96.3	0.047	0.056	0.031	0.998	13.8	3.1		21226

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	1.6	1.62	68.5		0.588	0.787	0.518	0.658		1.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6CCR	1.6	36.403	21165	1049	96.481	0.187	0.1856	0.2	0.2197	0.23	21.394

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]
0.735		-0.739	-0.593		0.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.43
r_dihedral_angle_4_deg	24.686
r_dihedral_angle_3_deg	12.812
r_dihedral_angle_1_deg	7.805
r_lrange_it	5.03
r_lrange_other	5.015
r_scangle_it	3.836
r_scangle_other	3.835
r_mcangle_it	2.998
r_mcangle_other	2.997
r_scbond_it	2.576
r_scbond_other	2.575
r_mcbond_it	1.985
r_mcbond_other	1.984
r_angle_refined_deg	1.67
r_angle_other_deg	1.458
r_nbd_refined	0.223
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.184
r_nbd_other	0.142
r_symmetry_nbd_refined	0.141
r_xyhbond_nbd_refined	0.12
r_symmetry_xyhbond_nbd_refined	0.116
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1353
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	13

Software

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