1YU9 | pdb_00001yu9

GppNHp-Bound Rab4A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Rab3a polyalanine

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	Ammonium sulfate, MES, Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.808	α = 90
b = 68.808	β = 90
c = 90.92	γ = 90

Symmetry
Space Group	P 43 21 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	IMAGE PLATE	MAR scanner 300 mm plate		2002-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

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	2.05	50	98.9	0.078	15.1	4		13803	1	1

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	2.05	2.11	98.9		0.282	4.1	4	2011

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	Rab3a polyalanine	2.07	7	25209	12656	665	98.58	0.179	0.1582	0.15631	0.17	0.19547	0.21	Random	16.527

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]
0.15			0.15		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.178
r_dihedral_angle_4_deg	15.99
r_dihedral_angle_3_deg	13.098
r_dihedral_angle_1_deg	6.016
r_scangle_it	2.425
r_scbond_it	1.543
r_angle_refined_deg	1.222
r_mcangle_it	0.963
r_mcbond_it	0.876
r_angle_other_deg	0.795
r_nbd_refined	0.204
r_symmetry_vdw_other	0.186
r_nbd_other	0.182
r_nbtor_refined	0.176
r_symmetry_hbond_refined	0.176
r_xyhbond_nbd_refined	0.157
r_symmetry_vdw_refined	0.136
r_mcbond_other	0.115
r_nbtor_other	0.081
r_chiral_restr	0.071
r_metal_ion_refined	0.037
r_bond_refined_d	0.008
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	1384
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	43

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement