X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.5
Details PROTEIN CONCENTRATION 20MG/ML, 2M AMMONIUM SULPHATE, 25% GLYCEROL AS CRYOPROTECTANT, pH 5.50

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.45 α = 90
b = 69.88 β = 90
c = 77.32 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 -- 1998-10-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A -- EMBL/DESY, HAMBURG BW7A

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
1.08 20 99.7 0.064 -- -- 4.3 -- 540161 -- -- --
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)
1.08 1.12 99.2 0.282 -- 5.0 3.5 --

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
OTHER 1.08 20.0 -- -- -- 119386 6334 99.2 -- 0.109 0.108 0.125 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 1.08 1.11 -- 460 8108 0.153 0.172 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 9.72
Anisotropic B[1][1] 1.3
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.55
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.695
r_scbond_it 2.595
r_mcangle_it 1.99
r_mcbond_it 1.382
r_nbd_refined 0.219
r_gen_planes_other 0.01
r_gen_planes_refined 0.012
r_chiral_restr 6.373
r_dihedral_angle_3_deg 2.087
r_angle_other_deg 1.912
r_bond_other_d 0.001
r_bond_refined_d 0.017
r_nbd_other 0.269
r_nbtor_other 0.082
r_xyhbond_nbd_refined 0.127
r_symmetry_vdw_refined 0.185
r_symmetry_vdw_other 0.312
r_symmetry_hbond_refined 0.127
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2377
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 510

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CCP4 Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
CCP4 model building