1UPT

Structure of a complex of the golgin-245 GRIP domain with Arl1


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.5
Details GROWTH IN 20% PEG 3350, 0.2M TRIS-HCL PH 8.5. RESERVOIR EXCHANGED FOR 31% PEG 3350, 31% PEG 3350, 0.2M TRIS-HCL PH 8.5, FROZEN IN 31% PEG 3350, 0.2M TRIS-HCL PH 8.5.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.5 α = 90
b = 89.71 β = 110.69
c = 72.53 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD TORROIDAL MIRROR 2003-05-15
Diffraction Radiation
Monochromator Protocol
SI111 MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.97925,0.97942,0.93928 ESRF ID14-4

Data Collection

Overall
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
1.7 67 98.7 0.062 -- -- 3.6 -- 94192 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.7 1.79 92.3 0.47 -- 1.0 3.1 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
DIRECT METHODS 1.7 67.42 -- -- -- 90538 3198 98.3 -- 0.222 0.221 0.252 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.7 1.74 -- 182 5526 0.349 0.392 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.97
Anisotropic B[1][1] -0.32
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.91
Anisotropic B[2][2] -0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.36
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.83
r_mcbond_it 0.906
r_bond_other_d 0.002
r_angle_refined_deg 1.486
r_xyhbond_nbd_refined 0.142
r_gen_planes_other 0.001
r_symmetry_vdw_other 0.329
r_symmetry_hbond_refined 0.13
r_dihedral_angle_1_deg 5.977
r_nbd_refined 0.211
r_bond_refined_d 0.014
r_metal_ion_refined 0.115
r_chiral_restr 0.08
r_symmetry_vdw_refined 0.136
r_nbd_other 0.229
r_scbond_it 2.41
r_nbtor_other 0.082
r_scangle_it 3.933
r_gen_planes_refined 0.005
r_mcangle_it 1.702
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7140
Nucleic Acid Atoms 0
Heterogen Atoms 132
Solvent Atoms 270

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
SnB phasing
SHARP phasing
REFMAC refinement version: 5.1.24