X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Small Tubes
pH 6.7
Temperature 289.0
Details 10 mM Bes, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.63 α = 90
b = 128.63 β = 90
c = 116.54 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2004-11-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 0.8123 EMBL/DESY, Hamburg X31

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
2.1 30 93.1 -- 0.085 -- 3.4 53619 53619 0.0 -3.0 25.3
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)
2.1 2.14 90.0 -- 0.444 5.8 3.1 2561

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
FOURIER SYNTHESIS 2.1 30.0 -- 0.0 50872 50872 2729 93.15 0.18536 0.18536 0.18382 0.21445 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 2.1 2.154 3599 184 3599 0.231 0.287 -- 89.99
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.624
Anisotropic B[1][1] 0.5
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.5
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.0
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.107
r_chiral_restr 0.074
r_symmetry_hbond_refined 0.086
r_dihedral_angle_4_deg 18.544
r_scbond_it 1.155
r_scangle_it 1.92
r_symmetry_vdw_refined 0.14
r_mcbond_it 0.529
r_bond_refined_d 0.007
r_dihedral_angle_3_deg 15.191
r_gen_planes_refined 0.003
r_nbd_refined 0.179
r_nbtor_refined 0.302
r_mcangle_it 0.891
r_dihedral_angle_1_deg 5.161
r_dihedral_angle_2_deg 34.236
r_angle_refined_deg 1.03
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati ESD (R-Free Set) 0.173
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6603
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 286

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling