X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 292.16
Details 1.2 M ammonium sulphate, 0.05 M N-(2-Acetamido)iminodiacetic Acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.16K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.12 α = 90
b = 100.12 β = 90
c = 169.65 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2006-04-07
Diffraction Radiation
Monochromator Protocol
Double crystal Si[111], horizontally focussing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 1.0 EMBL/DESY, Hamburg X12

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
2.6 20 99.3 0.118 -- -- 15.2 27047 27047 1.0 1.0 62.5
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)
2.6 2.64 98.0 -- -- 2.67 14.1 1291

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 2.6 19.63 -- -- 25612 25612 1356 99.2 0.21096 0.21096 0.2081 0.26681 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 2.6 2.666 1787 94 1787 0.268 0.293 -- 96.76
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 44.941
Anisotropic B[1][1] 1.46
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.93
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.012
r_angle_other_deg 0.907
r_scangle_it 4.22
r_nbd_other 0.203
r_nbtor_other 0.087
r_mcbond_it 0.812
r_bond_other_d 0.001
r_nbtor_refined 0.181
r_dihedral_angle_3_deg 16.992
r_gen_planes_other 0.001
r_symmetry_vdw_refined 0.192
r_mcbond_other 0.104
r_dihedral_angle_2_deg 37.592
r_nbd_refined 0.212
r_chiral_restr 0.08
r_gen_planes_refined 0.004
r_symmetry_hbond_refined 0.017
r_xyhbond_nbd_refined 0.163
r_dihedral_angle_1_deg 6.701
r_scbond_it 2.949
r_symmetry_vdw_other 0.192
r_angle_refined_deg 1.383
r_dihedral_angle_4_deg 19.807
r_mcangle_it 1.063
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5169
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 103

Software

Software
Software Name Purpose
MAR345dtb data collection
MOLREP phasing
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling