X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 295.0
Details 100mM bicine, 200mM MgCl2, 20% w/v PEG 8000 , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.66 α = 90
b = 66.36 β = 90
c = 115.34 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ cappilary optics 2005-01-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 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
1.59 20.38 99.7 0.073 -- -- 4.49 53416 53254 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)
1.593 1.634 100.0 0.03 -- 3.8 3.02 3785

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 1.593 20.38 0.0 0.0 53416 50573 2681 99.7 -- 0.20897 0.2068 0.24968 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 1.593 1.634 3785 184 3601 0.291 0.344 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 11.853
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_bond_other_d 0.002
r_nbtor_other 0.085
r_dihedral_angle_3_deg 13.392
r_scangle_it 2.944
r_symmetry_vdw_refined 0.326
r_xyhbond_nbd_refined 0.141
r_mcbond_other 0.233
r_scbond_it 2.241
r_mcbond_it 1.068
r_dihedral_angle_4_deg 21.704
r_symmetry_hbond_refined 0.203
r_nbtor_refined 0.172
r_dihedral_angle_1_deg 6.819
r_angle_refined_deg 1.553
r_mcangle_it 1.292
r_chiral_restr 0.097
r_dihedral_angle_2_deg 30.227
r_gen_planes_refined 0.006
r_gen_planes_other 0.001
r_bond_refined_d 0.015
r_nbd_other 0.209
r_symmetry_vdw_other 0.278
r_nbd_refined 0.188
r_angle_other_deg 0.931
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3443
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 466

Software

Software
Software Name Purpose
d*TREK data scaling
MOLREP phasing
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.004
CrystalClear data collection
MOSFLM data reduction
SCALA data scaling