6CD9 | pdb_00006cd9

GID4 in complex with a peptide

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CCR	early version of PDB entry 6ccr

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	24% PEG3350, 2.8% Tacsimate pH 7.0 and 0.1M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.27	α = 90
b = 40.022	β = 90
c = 110.727	γ = 90

Symmetry
Space Group	P 21 21 21

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	RIGAKU SATURN A200		2016-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	1.55	38.27	99.7	0.053	0.057	0.022	0.999	27.2	6.6		25493

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	1.55	1.58	98		0.423	0.463	0.186	0.891		6	1200

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	early version of PDB entry 6ccr	1.55	37.6	24168	1254	99.77	0.1744	0.1735	0.1833	0.1928	0.1977	12.43

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]
0.06			0.02		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.596
r_dihedral_angle_4_deg	26.601
r_dihedral_angle_3_deg	11.474
r_dihedral_angle_1_deg	6.791
r_mcangle_it	1.893
r_angle_refined_deg	1.633
r_mcbond_it	1.206
r_mcbond_other	1.202
r_angle_other_deg	0.975
r_chiral_restr	0.107
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1395
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	46

Software

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