X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 20% PEG 4000, 0.1M Tris-Cl PH 7.5, 0.02% NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.67 α = 90
b = 93.93 β = 92.94
c = 51.5 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD Bruker Platinum 135 Mirrors 2009-10-05
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER AXS MICROSTAR 1.5418 -- --

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
1.75 68.32 99.33 -- 0.341 -- 8.1 47731 47731 0.0 0.0 --
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)
1.75 1.84 93.9 0.4049 0.71 3.57 2.38 --

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 1.75 46.96 -- -- 47499 45093 2406 99.13 -- 0.21086 0.20721 0.28058 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 1.747 1.793 -- 164 3048 0.429 0.456 -- 91.51
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.814
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.93
r_nbtor_refined 0.313
r_dihedral_angle_3_deg 14.653
r_mcbond_it 1.116
r_dihedral_angle_4_deg 17.419
r_symmetry_hbond_refined 0.215
r_bond_refined_d 0.023
r_scbond_it 3.179
r_dihedral_angle_1_deg 5.935
r_gen_planes_refined 0.01
r_scangle_it 4.746
r_xyhbond_nbd_refined 0.224
r_mcangle_it 1.806
r_symmetry_vdw_refined 0.263
r_chiral_restr 0.129
r_nbd_refined 0.21
r_dihedral_angle_2_deg 32.644
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.241
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3572
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 845

Software

Software
Software Name Purpose
SAINT data scaling version: V7.34A
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
APEX data collection
SAINT data reduction