1W24 | pdb_00001w24

Crystal Structure Of human Vps29

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		25%PEG4000, 10%ETHYENE GLYCOL, 100MM HEPES PH7.5, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.19	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.871	α = 90
b = 53.871	β = 90
c = 124.2	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	MARRESEARCH		2004-06-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

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	2.1	30	96.5	0.07	4.6	4.5		10937		3

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	2.1	2.18	95.5		0.35	1.5	5.05

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.1	14.94	10289	573	97	0.219	0.218	0.222	0.244	0.2261	RANDOM	36.23

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]
0.02			0.02		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.905
r_scangle_it	2.88
r_mcangle_it	2.854
r_scbond_it	1.806
r_angle_refined_deg	1.774
r_mcbond_it	1.662
r_symmetry_vdw_refined	0.255
r_nbd_refined	0.249
r_xyhbond_nbd_refined	0.242
r_symmetry_hbond_refined	0.233
r_chiral_restr	0.133
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
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_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	1426
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
AUTOMAR	data reduction
MARSCALE	data scaling