1Z2X | pdb_00001z2x

Crystal structure of mouse Vps29

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	0.1M Tris, 0.2M NaCl, 20% PEG3000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.5	51.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.912	α = 90
b = 68.321	β = 106.98
c = 60.166	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	MARRESEARCH		2003-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.541

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	30	99.4	0.069	0.08	16.8	3.8		21420		6.3	25.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.3	99.4		0.216	0.252	6.3	3.7

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	MIR	THROUGHOUT	2.22	20	20185	1091	99.52	0.17591	0.17305	0.19	0.22765	0.24	RANDOM	25.347

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]
1.24		-1.42	-1.64		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.231
r_scangle_it	4.067
r_scbond_it	2.506
r_angle_refined_deg	1.829
r_mcangle_it	1.771
r_mcbond_it	0.964
r_angle_other_deg	0.939
r_nbd_other	0.248
r_symmetry_vdw_other	0.238
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.126
r_symmetry_hbond_refined	0.122
r_nbtor_other	0.09
r_bond_refined_d	0.019
r_gen_planes_other	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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	2892
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CCP4	data scaling
SHARP	phasing