7F68 | pdb_00007f68

Crystal structure of N-ras S89D

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UHV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		297	0.2 M ammonium sulphate, 0.1 M sodium acetate pH 4.6, 23% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.963	α = 90
b = 67.963	β = 90
c = 78.374	γ = 120

Symmetry
Space Group	P 32 2 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	CMOS	RDI CMOS_8M		2020-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.9792	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.24	50	97.6	0.158	0.164	0.042	5.7	12.8		57362

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	1.24	1.26	81.5		1.103	1.22	0.501	0.37		5.2

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	5uhv	1.24	27.57	54360	2966	96.81	0.1237	0.1226	0.1229	0.1443	0.1441	RANDOM	24.178

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]
1.04	0.52		1.04		-3.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.034
r_dihedral_angle_4_deg	21.899
r_dihedral_angle_3_deg	12.146
r_dihedral_angle_1_deg	6.124
r_rigid_bond_restr	2.675
r_angle_refined_deg	1.581
r_angle_other_deg	1.521
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1350
Nucleic Acid Atoms
Solvent Atoms	226
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing