X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.7
Details 5MG/ML 0.1 M MES/NAOH PH 5.7,, 4.5% W/V PEG 3350, 25 MM SODIUM NITRATE, 10% V/V GLYCEROL, 10 DEGREES CELSIUS

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.73 α = 90
b = 100.73 β = 90
c = 60.3 γ = 90
Symmetry
Space Group I 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD (QUANTUM 315R) ADSC -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 -- ESRF ID23-1

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
2.3 71.23 98.0 0.04 -- -- 3.6 -- 13277 -- 1.0 --
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)
2.3 2.36 98.6 0.37 -- 3.9 3.8 --

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 2.31 71.23 -- -- -- 12395 680 97.9 -- 0.21033 0.20668 0.27734 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 2.311 2.371 -- 60 884 0.292 0.428 -- 98.64
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.949
Anisotropic B[1][1] 2.42
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.83
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 0.063
r_scbond_it 0.047
r_mcangle_it 0.057
r_mcbond_other 0.013
r_mcbond_it 0.037
r_nbd_refined 0.211
r_gen_planes_other 0.001
r_gen_planes_refined 0.004
r_chiral_restr 0.079
r_dihedral_angle_4_deg 17.102
r_dihedral_angle_3_deg 18.916
r_dihedral_angle_2_deg 34.838
r_dihedral_angle_1_deg 6.243
r_angle_other_deg 0.948
r_angle_refined_deg 1.354
r_bond_other_d 0.001
r_bond_refined_d 0.011
r_nbd_other 0.201
r_nbtor_refined 0.18
r_nbtor_other 0.09
r_xyhbond_nbd_refined 0.152
r_xyhbond_nbd_other 0.025
r_symmetry_vdw_refined 0.13
r_symmetry_vdw_other 0.249
r_symmetry_hbond_refined 0.059
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2048
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 86

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
REFMAC 5.2.0019G Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019G refinement