2J1L

Crystal Structure of Human Rho-related GTP-binding protein RhoD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MH1	PDB ENTRY 1MH1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		19% PEG6K, 0.4M NH4CL, 15% ETG, 0.05M MES PH6.0, pH 6.00

Crystal Properties
Matthews coefficient	Solvent content
2.79	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.811	α = 90
b = 66.81	β = 90
c = 103.921	γ = 120

Symmetry
Space Group	P 31 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	CCD	MARRESEARCH		2006-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	2.5	50.6	100	0.09	16.8	8.1		9805			82.9

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	2.5	2.62	100		0.66	2.3	5.3

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1MH1	2.5	50	9279	467	100	0.219	0.217	0.242	RANDOM	51.86

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]
3.5	1.75		3.5		-5.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.856
r_dihedral_angle_4_deg	23.31
r_dihedral_angle_3_deg	16.431
r_dihedral_angle_1_deg	6.389
r_scangle_it	2.128
r_angle_refined_deg	1.401
r_scbond_it	1.353
r_mcangle_it	0.923
r_angle_other_deg	0.894
r_mcbond_it	0.499
r_nbd_refined	0.23
r_nbd_other	0.185
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.145
r_symmetry_vdw_other	0.097
r_symmetry_vdw_refined	0.093
r_nbtor_other	0.086
r_chiral_restr	0.074
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1160
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing