1ZVQ | pdb_00001zvq

Structure of the Q61G mutant of Ras in the GDP-bound form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Q21	PDB ENTRY 4Q21

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	18% PEG4000, 50 mM Ca Acetate, 10 mM MgCl2, 100 mM Tris-HCl, 250 mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.992	α = 90
b = 92.992	β = 90
c = 121.015	γ = 120

Symmetry
Space Group	H 3 2

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	ADSC QUANTUM 4	Monochromator	2004-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.00	NSLS	X26C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	38.2	98.8	0.078	24.1	7.1	13906	13739		2	26.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	91.8	79.5	0.497	2.6	3.1	1257

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 4Q21	2	38.2	13906	13049	690	98.79	0.188	0.188	0.186	0.188	0.229	0.2331	RANDOM	30.795

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]
-1.56	-0.78		-1.56		2.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.557
r_dihedral_angle_4_deg	18.367
r_dihedral_angle_3_deg	14.62
r_dihedral_angle_1_deg	5.638
r_scangle_it	2.758
r_scbond_it	1.757
r_angle_refined_deg	1.268
r_mcangle_it	1.054
r_mcbond_it	0.672
r_nbtor_refined	0.306
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.155
r_xyhbond_nbd_refined	0.138
r_symmetry_hbond_refined	0.114
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1317
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	30

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing