X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 293.0
Details PEG MME550, NaCl, Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.45 α = 90
b = 80.45 β = 90
c = 172.17 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Synchrotron 2002-02-15
Diffraction Radiation
Monochromator Protocol
SYNCHROTRON SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.3 1.0 ALS 5.0.3

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
1.6 44 98.0 -- 0.086 -- 7.4 32234 28879 2.0 2.0 38.15
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)
1.9 1.95 93.0 0.578 -- -- -- 1557

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 1.9 40.0 0.0 0.0 28879 25106 1337 98.45 0.229 0.22689 0.22454 0.27259 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 1.9 1.949 -- 95 1557 0.321 0.365 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.157
Anisotropic B[1][1] -1.14
Anisotropic B[1][2] -0.57
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.71
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.003
r_symmetry_hbond_refined 0.693
r_bond_other_d 0.002
r_mcangle_it 1.612
r_symmetry_vdw_refined 0.467
r_scbond_it 2.459
r_bond_refined_d 0.013
r_nbtor_other 0.091
r_chiral_restr 0.084
r_mcbond_it 0.821
r_nbd_refined 0.203
r_nbd_other 0.243
r_angle_other_deg 0.839
r_xyhbond_nbd_refined 0.16
r_scangle_it 4.161
r_angle_refined_deg 1.468
r_gen_planes_refined 0.007
r_symmetry_vdw_other 0.308
r_dihedral_angle_1_deg 7.693
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.161
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2105
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 72

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
AMoRE phasing
REFMAC refinement version: 5.1.19
CCP4 data scaling version: (SCALA)