X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 292.0
Details 0.1 M sodium acetate, 0.2 M ammonium acetate, 25% PEG 4000, 15 mM glucose, streak seeding, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.36 α = 90
b = 49.06 β = 103.56
c = 82.62 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
FLAT PANEL MAR555 FLAT PANEL mirrors 2007-02-04
Diffraction Radiation
Monochromator Protocol
Ge(111) triangular bent crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8148 EMBL/DESY, Hamburg X11

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
1.26 40 95.4 0.059 -- -- 4.6 151662 151662 -- -3.0 12.9
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)
1.26 1.31 93.8 0.467 -- 2.0 3.3 14787

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 1.26 19.54 -- -- 149903 149903 1654 95.04 0.14277 0.14277 0.14235 0.18244 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 1.26 1.29 10372 119 10372 0.221 0.278 -- 89.75
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic model of ADP parameters
Mean Isotropic B 9.348
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.22
r_symmetry_vdw_refined 0.156
r_bond_other_d 0.001
r_angle_other_deg 1.044
r_mcbond_other 0.933
r_sphericity_bonded 5.096
r_mcangle_it 2.493
r_sphericity_free 10.821
r_dihedral_angle_3_deg 11.999
r_dihedral_angle_4_deg 15.339
r_nbtor_refined 0.191
r_symmetry_hbond_refined 0.111
r_dihedral_angle_2_deg 33.975
r_rigid_bond_restr 1.807
r_nbd_other 0.173
r_xyhbond_nbd_refined 0.111
r_angle_refined_deg 1.744
r_mcbond_it 2.097
r_scbond_it 3.554
r_chiral_restr 0.119
r_symmetry_vdw_other 0.264
r_gen_planes_other 0.001
r_scangle_it 4.627
r_bond_refined_d 0.018
r_nbtor_other 0.088
r_gen_planes_refined 0.01
r_dihedral_angle_1_deg 6.297
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5091
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 763

Software

Software
Software Name Purpose
MAR345dtb data collection
MOLREP phasing
REFMAC refinement version: 5.2.0003
DENZO data reduction
SCALEPACK data scaling