X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5
Details 9% (W/V) PEG 4000, 0.1 M NA ACETATE PH 5.0, 1-8% GLYCEROL, 100 MM DHAP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.4 α = 90
b = 157.3 β = 108.2
c = 101.5 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
-- -- -- 2002-02-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B -- EMBL/DESY, HAMBURG BW7B

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
2.1 40 90.2 0.071 -- -- 3.6 -- 125363 -- -- --
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)
2.1 2.19 59.3 0.272 -- 2.3 2.1 --

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
MOLECULAR REPLACEMENT 2.1 36.51 -- -- -- 125363 3203 100.0 -- 0.164 0.163 0.185 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 2.1 2.15 -- 158 5639 0.249 0.26 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.04
Anisotropic B[1][1] -0.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.07
Anisotropic B[2][2] -0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.24
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.916
r_scbond_it 2.199
r_mcangle_it 1.295
r_mcbond_it 0.603
r_nbd_refined 0.202
r_gen_planes_other 0.003
r_gen_planes_refined 0.005
r_chiral_restr 0.079
r_dihedral_angle_1_deg 5.666
r_angle_other_deg 0.834
r_angle_refined_deg 1.275
r_bond_other_d 0.003
r_bond_refined_d 0.013
r_nbd_other 0.239
r_nbtor_other 0.086
r_xyhbond_nbd_refined 0.15
r_symmetry_vdw_refined 0.327
r_symmetry_vdw_other 0.37
r_symmetry_hbond_refined 0.255
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19358
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 641

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement