2RKO | pdb_00002rko

Crystal Structure of the Vps4p-dimer

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XWI	PDB ENTRY 1XWI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.9	292	0.1M MES, 0.8M-1.9M MgSO4, pH 5.9-6.5, VAPOR DIFFUSION, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
4.14	70.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.116	α = 90
b = 109.116	β = 90
c = 176.632	γ = 120

Symmetry
Space Group	P 65 2 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	CCD	MARMOSAIC 225 mm CCD		2005-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	3.35	94.498	99.4	0.057	0.057	22.6	8.1		9446

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	3.35	3.53	100		0.44	0.44	4.9	8.4	1345

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 ENTRY 1XWI	3.35	30	9386	471	99.19	0.27	0.268	0.3	0.298	0.35	RANDOM	88.089

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]
2.29	1.15		2.29		-3.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.438
r_dihedral_angle_3_deg	18.419
r_dihedral_angle_4_deg	9.295
r_scangle_it	7.976
r_scbond_it	5.69
r_dihedral_angle_1_deg	5.129
r_mcangle_it	3.813
r_mcbond_it	2.767
r_angle_refined_deg	1.107
r_angle_other_deg	0.83
r_mcbond_other	0.502
r_nbd_refined	0.26
r_symmetry_vdw_other	0.24
r_nbd_other	0.208
r_nbtor_refined	0.189
r_symmetry_vdw_refined	0.176
r_xyhbond_nbd_refined	0.164
r_symmetry_hbond_refined	0.112
r_xyhbond_nbd_other	0.097
r_nbtor_other	0.09
r_chiral_restr	0.05
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2173
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
REFMAC	refinement