X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.5
Details 100MM NA-CITRATE 5.6, 30% PEG 4000,200MM AMMONIUM ACETATE, pH 5.50

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.96 α = 90
b = 193.59 β = 90
c = 92.69 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC MIRRORS 2000-08-15
Diffraction Radiation
Monochromator Protocol
SI CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 -- ESRF ID14-2

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
2.5 29.78 96.1 0.062 -- -- 2.6 -- 53292 -- -- --
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)
2.5 2.63 90.0 0.195 -- 2.0 2.4 --

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 2.5 29.75 -- -- -- 53292 2840 100.0 -- 0.181 0.178 0.237 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 2.5 2.56 -- 186 3527 0.217 0.313 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.89
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.107
r_scbond_it 1.273
r_mcangle_it 1.087
r_mcbond_it 0.577
r_nbd_refined 0.197
r_gen_planes_other 0.003
r_gen_planes_refined 0.004
r_chiral_restr 0.102
r_dihedral_angle_1_deg 6.156
r_angle_other_deg 0.819
r_angle_refined_deg 1.183
r_bond_other_d 0.002
r_bond_refined_d 0.01
r_nbd_other 0.225
r_nbtor_other 0.084
r_xyhbond_nbd_refined 0.172
r_metal_ion_refined 0.106
r_symmetry_vdw_refined 0.18
r_symmetry_vdw_other 0.216
r_symmetry_hbond_refined 0.145
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11910
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 362

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
MOLREP, CNS, COMO, AMORE , EPMR, XFIT, O Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
O model building
XFIT model building
EPMR model building
AMORE model building
COMO model building
CNS model building
MOLREP model building