3LAW | pdb_00003law

Structure of GTP-bound L129F mutant Rab7

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	291	0.2 M sodium formate, 10mM trimethylamine hydrochloride, and 20% polyethylene glycol 3,350, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.554	α = 71.24
b = 89.335	β = 85.97
c = 89.378	γ = 85.91

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1.0	NSLS	X6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.8	20	98.7	0.1	7.7	2	24170	23869	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.871	98.2		0.417	1.7	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.8	19.88	24300	23869	1277	98.7	0.23678	0.22036	0.22	0.27265	0.28	RANDOM	29.888

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]
-2.02	0.35	0.09	0.75	-1.21	1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.853
r_dihedral_angle_4_deg	20.412
r_dihedral_angle_3_deg	20.314
r_dihedral_angle_1_deg	6.636
r_scangle_it	2.423
r_scbond_it	1.466
r_mcangle_it	1.269
r_angle_refined_deg	1.175
r_mcbond_it	0.722
r_nbtor_refined	0.321
r_symmetry_hbond_refined	0.295
r_nbd_refined	0.245
r_symmetry_vdw_refined	0.243
r_xyhbond_nbd_refined	0.163
r_metal_ion_refined	0.088
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7044
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	165

Software

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