X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 292.0
Details PEG 4000, PEG 400, magnesium chloride, Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.3 α = 90
b = 77.62 β = 90
c = 148.15 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Toroidal mirror 1999-11-04
Diffraction Radiation
Monochromator Protocol
Double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 1.0442 EMBL/DESY, Hamburg X31

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
1.65 20 -- 0.075 -- -- 5.6 70249 70249 0.0 -3.0 --
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)
1.65 1.68 89.9 0.476 -- 2.5 5.5 --

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
MOLECULAR REPLACEMENT 1.65 19.5 -- -- 69077 69077 1064 99.52 -- 0.16349 0.16295 0.19836 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 1.65 1.694 -- 79 4802 0.252 0.261 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 10.18
Anisotropic B[1][1] -0.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.42
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.187
r_dihedral_angle_3_deg 15.832
r_nbd_refined 0.3
r_angle_refined_deg 1.411
r_dihedral_angle_1_deg 3.992
r_mcangle_it 1.011
r_bond_refined_d 0.009
r_gen_planes_other 0.003
r_bond_other_d 0.001
r_metal_ion_refined 0.099
r_symmetry_hbond_other 0.08
r_symmetry_vdw_other 0.223
r_mcbond_it 0.529
r_nbtor_other 0.821
r_symmetry_vdw_refined 0.181
r_nbd_other 0.212
r_angle_other_deg 1.105
r_scangle_it 2.961
r_chiral_restr 0.073
r_xyhbond_nbd_other 0.162
r_scbond_it 1.763
r_gen_planes_refined 0.004
r_xyhbond_nbd_refined 0.149
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.085
Luzzati ESD (R-Free Set) 0.088
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4240
Nucleic Acid Atoms 0
Heterogen Atoms 11
Solvent Atoms 575

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
EPMR phasing
REFMAC refinement version: 5.0