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_sphericity_bonded 5.096
r_sphericity_free 10.821
r_rigid_bond_restr 1.807
r_scangle_it 4.627
r_scbond_it 3.554
r_mcangle_it 2.493
r_mcbond_other 0.933
r_mcbond_it 2.097
r_nbd_refined 0.22
r_gen_planes_other 0.001
r_gen_planes_refined 0.01
r_chiral_restr 0.119
r_dihedral_angle_4_deg 15.339
r_dihedral_angle_3_deg 11.999
r_dihedral_angle_2_deg 33.975
r_dihedral_angle_1_deg 6.297
r_angle_other_deg 1.044
r_angle_refined_deg 1.744
r_bond_other_d 0.001
r_bond_refined_d 0.018
r_nbd_other 0.173
r_nbtor_refined 0.191
r_nbtor_other 0.088
r_xyhbond_nbd_refined 0.111
r_symmetry_vdw_refined 0.156
r_symmetry_vdw_other 0.264
r_symmetry_hbond_refined 0.111
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

Computing
Computing Package Purpose
MAR345dtb Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0003 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0003 refinement
MOLREP model building
MAR345dtb data collection