7DPJ | pdb_00007dpj

H-Ras Q61L in complex with GppNHp (state 1) after structural transition by humidity control

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K8Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PEG400, SODIUM ACETATE, CALCIUM ACETATE

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.844	α = 90
b = 91.844	β = 90
c = 121.413	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 315r		2016-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

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	1.976	45.93	99.9	0.122	37.5	10.6		14025

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	1.976	2			0.462

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3k8y	1.976	45.93	14025	1408	99.915	0.193	0.1895	0.19	0.221	0.22	22.144

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]
-0.003	-0.001		-0.003		0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.367
r_dihedral_angle_4_deg	20.432
r_dihedral_angle_3_deg	12.558
r_dihedral_angle_1_deg	6.203
r_lrange_it	4.407
r_lrange_other	4.27
r_scangle_other	2.612
r_scangle_it	2.609
r_mcangle_it	2.118
r_mcangle_other	2.117
r_scbond_other	1.611
r_scbond_it	1.609
r_angle_refined_deg	1.376
r_mcbond_it	1.296
r_mcbond_other	1.294
r_angle_other_deg	1.275
r_symmetry_nbd_refined	0.312
r_symmetry_metal_ion_refined	0.214
r_metal_ion_refined	0.208
r_nbd_refined	0.206
r_symmetry_nbd_other	0.181
r_nbd_other	0.18
r_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.15
r_symmetry_xyhbond_nbd_refined	0.131
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.052
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1258
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing