7DPH | pdb_00007dph

H-Ras Q61H 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	5	293	PEG400, SODIUM ACETATE, CALCIUM ACETATE

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.769	α = 90
b = 91.769	β = 90
c = 121.268	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		2018-01-21	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	1.54	50	99.8	0.043	68.4	10.4		29269

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	1.54	1.57			0.333	9.3

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	1.54	23.208	29199	1406	99.761	0.193	0.1922	0.2	0.2023	0.21	17.994

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]
					-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.456
r_dihedral_angle_4_deg	19.473
r_dihedral_angle_3_deg	12.777
r_dihedral_angle_1_deg	6.128
r_lrange_it	3.522
r_lrange_other	3.405
r_scangle_other	1.604
r_scangle_it	1.602
r_mcangle_it	1.493
r_mcangle_other	1.493
r_angle_refined_deg	1.293
r_angle_other_deg	1.25
r_scbond_it	0.985
r_scbond_other	0.984
r_mcbond_it	0.85
r_mcbond_other	0.841
r_nbd_refined	0.201
r_symmetry_xyhbond_nbd_refined	0.183
r_metal_ion_refined	0.181
r_symmetry_nbd_other	0.178
r_symmetry_nbd_refined	0.155
r_nbtor_refined	0.147
r_xyhbond_nbd_refined	0.147
r_nbd_other	0.139
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.054
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1234
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	35

Software

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