X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8
Details 35% (W/V) PEG 3350, 500 MM SODIUM NITRATE, 5 MM DITHIOTHREITOL, 40 MM N-ACETYL-LACTOSAMINE, 10 MM TRIS-HCL 8.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.45 α = 90
b = 43.65 β = 105.82
c = 63.9 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR555 FLAT PANEL BENT, VERTICALLY FOCUSSING MIRROR 2009-02-17
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 -- 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
1.91 35 98.0 0.1 -- -- 2.7 -- 22025 -- 2.0 25.423
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)
1.91 2.01 98.5 0.31 -- 2.7 2.7 --

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 1.91 35.0 -- -- -- 20895 1126 97.45 -- 0.18443 0.18163 0.23799 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 1.91 2.013 -- 148 3071 0.27 0.337 -- 98.02
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.591
Anisotropic B[1][1] -1.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.31
Anisotropic B[2][2] 2.13
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.87
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.012
r_dihedral_angle_3_deg 13.064
r_nbd_refined 0.193
r_scangle_it 5.351
r_dihedral_angle_4_deg 20.04
r_angle_other_deg 0.857
r_dihedral_angle_1_deg 6.897
r_gen_planes_other 0.001
r_dihedral_angle_2_deg 37.303
r_chiral_restr 0.091
r_mcbond_it 2.536
r_gen_planes_refined 0.006
r_scbond_it 3.843
r_xyhbond_nbd_refined 0.137
r_symmetry_vdw_refined 0.164
r_angle_refined_deg 1.345
r_nbtor_other 0.081
r_nbtor_refined 0.168
r_symmetry_vdw_other 0.231
r_symmetry_hbond_refined 0.09
r_mcangle_it 3.443
r_mcbond_other 0.928
r_nbd_other 0.186
r_bond_other_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2354
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 163

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0070
MOSFLM data reduction
SCALA data scaling
PHASER phasing