4CYM | pdb_00004cym

Complex of human VARP-ANKRD1 with Rab32-GppCp

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YHN	PDB ENTRIES 1YHN AND 4B93
experimental model	PDB	4B93	PDB ENTRIES 1YHN AND 4B93

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.445	α = 90
b = 144.445	β = 90
c = 135.68	γ = 120

Symmetry
Space Group	P 32 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	PIXEL	DECTRIS PILATUS 6M		2012-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

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	2.8	72.22	98.8	0.24	8.8	7.4		40077

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	2.8	2.91	94.1		1.5	0.9	5

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 ENTRIES 1YHN AND 4B93	2.8	125.09	38004	2011	98.33	0.19466	0.19205	0.2006	0.24565	0.2465	RANDOM	74.856

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]
1.4	0.7		1.4		-4.53

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_other	11.745
r_long_range_B_refined	11.743
r_scangle_other	8.749
r_mcangle_it	8.083
r_mcangle_other	8.083
r_scbond_it	5.522
r_scbond_other	5.522
r_mcbond_it	5.212
r_mcbond_other	5.2
r_angle_refined_deg	1.539
r_angle_other_deg	1.076
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.004
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8052
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	99

Software

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