X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6
Temperature 293.0
Details PEG 4000, imidazol-malate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.41 α = 90
b = 54.08 β = 96.12
c = 109.75 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
CCD MARRESEARCH -- 2003-01-24
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.9881,0.9809,0.815 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
1.95 20 91.6 -- 0.053 -- 4.3 -- 55200 -- -- --
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)
1.95 2.0 67.0 -- 0.311 2.3 1.5 --

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
MAD 1.95 12.0 -- -- 54975 53883 1092 91.66 -- 0.17775 0.17688 0.21932 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 1.95 1.999 -- 49 2826 0.27 0.328 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.675
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.14
Anisotropic B[2][2] 1.77
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.7
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.817
r_bond_refined_d 0.009
r_gen_planes_refined 0.004
r_nbd_other 0.232
r_nbtor_other 0.08
r_symmetry_vdw_refined 0.155
r_mcbond_it 0.793
r_scbond_it 1.679
r_dihedral_angle_1_deg 6.765
r_mcangle_it 1.494
r_angle_refined_deg 1.188
r_bond_other_d 0.002
r_angle_other_deg 0.769
r_symmetry_hbond_refined 0.465
r_symmetry_vdw_other 0.247
r_xyhbond_nbd_refined 0.151
r_chiral_restr 0.073
r_nbd_refined 0.194
r_gen_planes_other 0.003
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.163
Luzzati ESD (R-Free Set) 0.15
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5513
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 331

Software

Software
Software Name Purpose
DENZO data reduction
SCALA data scaling
SOLVE phasing
REFMAC refinement version: 5.1.24
CCP4 data scaling version: (SCALA)