3CON | pdb_00003con

Crystal structure of the human NRAS GTPase bound with GDP

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, SITTING DROP	8.5	291	30.0% PEG 3350, 0.2M Magnesium chloride, 0.1 M Tris-HCl, GDP was added to the concentrated protein to a final concentration of 5mM. Crystallization were set up with 1:100 chymotrypsin, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.78	30.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.061	α = 90
b = 83.061	β = 90
c = 38.907	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS		2008-03-13	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.649	40	99.2	0.065	13.9	9.7		18539

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.649	1.71	92.8		0.469		4.6	1710

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	PDB entry 4Q21	1.649	35.967	18528	949	99.16	0.186	0.185	0.2	0.219	0.22	RANDOM	19.437

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]
-0.056	-0.028		-0.056		0.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.808
r_dihedral_angle_4_deg	14.187
r_dihedral_angle_3_deg	11.594
r_dihedral_angle_1_deg	5.722
r_scangle_it	3.879
r_mcangle_it	3.021
r_scbond_it	2.846
r_mcbond_it	2.396
r_angle_refined_deg	1.53
r_angle_other_deg	0.943
r_mcbond_other	0.693
r_symmetry_vdw_other	0.26
r_nbd_refined	0.211
r_nbd_other	0.204
r_nbtor_refined	0.176
r_symmetry_vdw_refined	0.128
r_symmetry_hbond_refined	0.115
r_xyhbond_nbd_refined	0.108
r_chiral_restr	0.091
r_nbtor_other	0.083
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1216
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	40

Software

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