X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 100.0
Details MPD, Calcium Chloride, Tris, pH 9.00, VAPOR DIFFUSION, HANGING DROP, temperature 100K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.9 α = 90
b = 74.2 β = 90
c = 134.82 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 MAR scanner 345 mm plate MIRRORS 2001-12-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 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
2.07 41.1 94.5 0.06 -- -- 3.0 89732 30610 1.0 1.0 28.0
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)
2.07 2.14 60.0 -- -- -- -- --

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 2.07 41.17 -- -- 30610 29010 1551 94.04 -- 0.15874 0.15623 0.20585 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 2.07 2.124 -- 73 1221 0.371 0.421 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.753
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_refined_d 0.016
r_scangle_it 3.477
r_mcbond_it 0.791
r_angle_other_deg 0.92
r_symmetry_vdw_other 0.299
r_dihedral_angle_1_deg 6.949
r_xyhbond_nbd_refined 0.165
r_chiral_restr 0.098
r_gen_planes_refined 0.007
r_nbtor_other 0.087
r_mcangle_it 1.432
r_symmetry_hbond_refined 0.164
r_bond_other_d 0.002
r_nbd_refined 0.199
r_gen_planes_other 0.006
r_symmetry_vdw_refined 0.074
r_angle_refined_deg 1.547
r_nbd_other 0.246
r_scbond_it 2.225
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.216
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3949
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 324

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.1.24
AMoRE phasing