X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 289.0
Details 20% PEG 3350, 0.2M NH4Cl, 0.02M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.6 α = 90
b = 57.01 β = 102.04
c = 60.6 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
IMAGE PLATE MAR555 FLAT PANEL Mirrors 2009-07-31
Diffraction Radiation
Monochromator Protocol
Si (111), horizontally focussing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8150 EMBL/DESY, Hamburg X11

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 20.67 99.6 0.078 0.078 -- 2.9 -- 29594 3.0 3.0 25.4
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 99.8 0.28 0.28 2.0 3.1 4288

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 1.7 20.24 -- 0.0 29594 27296 893 91.54 0.18 0.18 0.18 0.204 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 1.701 1.745 -- 43 1242 0.34 0.29 -- 59.11
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.72
Anisotropic B[1][1] 0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.22
Anisotropic B[2][2] -0.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.27
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 15.692
r_chiral_restr 0.074
r_bond_refined_d 0.008
r_gen_planes_refined 0.004
r_scbond_it 1.147
r_angle_refined_deg 1.042
r_dihedral_angle_1_deg 5.33
r_dihedral_angle_2_deg 31.565
r_dihedral_angle_3_deg 11.408
r_mcangle_it 0.795
r_mcbond_it 0.423
r_scangle_it 1.876
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2398
Nucleic Acid Atoms 0
Heterogen Atoms 64
Solvent Atoms 214

Software

Software
Software Name Purpose
SCALA data scaling version: 3.2.25
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
MAR345dtb data collection
AUTOMAR data reduction