3CBQ | pdb_00003cbq

Crystal structure of the human REM2 GTPase with bound GDP

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	20% PEG 3350, 0.2M KCl, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.72	28.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.143	α = 90
b = 64.33	β = 90
c = 73.204	γ = 90

Symmetry
Space Group	C 2 2 21

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		2008-02-07	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	1.82	25	99.8	0.074	10.6	6.9		13866

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)
	1.82	1.89	99		0.658		6.5	1364

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 2GJS	1.82	22.71	13840	679	99.81	0.192	0.19	0.19	0.249	0.24	RANDOM	20.115

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]
-1.33			1.97		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.629
r_dihedral_angle_4_deg	19.485
r_dihedral_angle_3_deg	11.281
r_dihedral_angle_1_deg	5.693
r_scangle_it	3.574
r_mcangle_it	3.214
r_mcbond_it	2.656
r_scbond_it	2.623
r_angle_refined_deg	1.437
r_angle_other_deg	0.922
r_mcbond_other	0.76
r_symmetry_vdw_other	0.266
r_nbd_other	0.203
r_nbd_refined	0.194
r_nbtor_refined	0.167
r_symmetry_hbond_refined	0.154
r_xyhbond_nbd_refined	0.128
r_xyhbond_nbd_other	0.107
r_chiral_restr	0.084
r_nbtor_other	0.083
r_symmetry_vdw_refined	0.072
r_metal_ion_refined	0.052
r_bond_refined_d	0.016
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	1309
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms	38

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling