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_scbond_it 1.679
r_mcangle_it 1.494
r_nbd_refined 0.194
r_gen_planes_other 0.003
r_gen_planes_refined 0.004
r_chiral_restr 0.073
r_dihedral_angle_1_deg 6.765
r_angle_other_deg 0.769
r_angle_refined_deg 1.188
r_bond_other_d 0.002
r_bond_refined_d 0.009
r_nbd_other 0.232
r_nbtor_other 0.08
r_xyhbond_nbd_refined 0.151
r_symmetry_vdw_refined 0.155
r_symmetry_vdw_other 0.247
r_symmetry_hbond_refined 0.465
r_mcbond_it 0.793
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

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