3C5C | pdb_00003c5c

Crystal structure of human Ras-like, family 12 protein in complex with GDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ATV	pdb entry 2ATV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	291	0.1 M Tris-HCl pH 8.5, 28% PEG 4000, 0.2 M Magnesium chloride. In situ proteolysis with 1:100 endoproteinase Glu-C V8, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.04	α = 101.46
b = 66.436	β = 90.03
c = 71.943	γ = 89.89

Symmetry
Space Group	P 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	IMAGE PLATE	RIGAKU RAXIS		2007-12-18	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	1.85	40	98.9	0.119	7.1	4.3		52667

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)
	1.85	1.92	95.6		0.955		3.9	5090

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 2ATV	1.85	30	52136	2062	98.89	0.203	0.202	0.2	0.238	0.24	thin shells	18.47

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]
-1.1	-0.13	0.14	0.4	0.01	0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.235
r_dihedral_angle_4_deg	13.435
r_dihedral_angle_3_deg	12.594
r_dihedral_angle_1_deg	6.305
r_scangle_it	3.14
r_mcangle_it	3.041
r_scbond_it	2.28
r_mcbond_it	2.244
r_angle_refined_deg	1.329
r_angle_other_deg	1.061
r_mcbond_other	0.636
r_symmetry_vdw_other	0.289
r_symmetry_vdw_refined	0.206
r_nbd_refined	0.205
r_nbd_other	0.203
r_nbtor_refined	0.171
r_symmetry_hbond_refined	0.169
r_xyhbond_nbd_refined	0.14
r_nbtor_other	0.092
r_chiral_restr	0.078
r_metal_ion_refined	0.038
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5187
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	122

Software

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