X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 295.0
Details 1.7M AMMONIUM SULFATE, 2% PEG 400, 100MM NA HEPES, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.21 α = 90
b = 81.22 β = 90
c = 123.36 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 RIGAKU VARIMAX CONFOCAL OPTICS 2005-01-26
Diffraction Radiation
Monochromator Protocol
RIGAKU VARIMAX OPTICS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 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
2 49.12 81.3 0.048 -- -- 4.03 44340 36317 -- -- 39.0
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)
2.0 2.07 82.3 0.29 -- 4.6 4.0 4379

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 2.0 20.0 -- -- -- 34473 1801 81.91 -- 0.19895 0.19651 0.24567 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 2.0 2.051 -- 137 2514 0.262 0.343 -- 83.36
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.876
Anisotropic B[1][1] 0.28
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.21
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.086
r_gen_planes_refined 0.003
r_xyhbond_nbd_refined 0.11
r_mcbond_it 1.222
r_scangle_it 4.102
r_mcangle_it 1.853
r_dihedral_angle_4_deg 17.903
r_dihedral_angle_3_deg 14.123
r_nbd_refined 0.186
r_bond_refined_d 0.007
r_nbtor_refined 0.29
r_dihedral_angle_1_deg 5.881
r_chiral_restr 0.068
r_scbond_it 2.939
r_symmetry_vdw_refined 0.169
r_symmetry_hbond_refined 0.104
r_dihedral_angle_2_deg 37.468
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.289
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4636
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 261

Software

Software
Software Name Purpose
CrystalClear data collection
CNS refinement
REFMAC refinement version: 5.2.0019
d*TREK data reduction
d*TREK data scaling
CNS phasing