1Z9O | pdb_00001z9o

1.9 Angstrom Crystal Structure of the Rat VAP-A MSP Homology Domain in Complex with the Rat ORP1 FFAT Motif

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Z9L	Found Se by molecular replacement w/ 1Z9L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	283	PEG 2000 MME, sodium thiocyanate, tris buffer, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.048	α = 90.01
b = 50.033	β = 90
c = 90.287	γ = 60.03

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	100	CCD	ADSC QUANTUM 4		2004-08-28	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 4		2004-08-28	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0331	ALS	8.2.1
2	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9794	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	50			4	59859	59506	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.9	1.949	100

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	Found Se by molecular replacement w/ 1Z9L	1.9	14.65	53477	53477	6029	100	0.21941	0.21472	0.23	0.26051	RANDOM	26.342

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]
1.01	-0.45	0.05	1	-0.02	-1.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.45
r_dihedral_angle_3_deg	19.326
r_dihedral_angle_4_deg	19.094
r_dihedral_angle_1_deg	7.322
r_scangle_it	4.613
r_scbond_it	3.466
r_angle_refined_deg	2.492
r_mcangle_it	2.093
r_mcbond_it	1.786
r_angle_other_deg	1.135
r_mcbond_other	0.504
r_symmetry_vdw_other	0.305
r_xyhbond_nbd_refined	0.22
r_nbd_other	0.215
r_symmetry_vdw_refined	0.199
r_nbd_refined	0.192
r_nbtor_refined	0.192
r_symmetry_hbond_refined	0.183
r_chiral_restr	0.153
r_xyhbond_nbd_other	0.107
r_nbtor_other	0.102
r_bond_refined_d	0.031
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6144
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing