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_nbtor_other 0.087
r_nbd_other 0.246
r_nbd_refined 0.199
r_gen_planes_other 0.006
r_gen_planes_refined 0.007
r_chiral_restr 0.098
r_dihedral_angle_1_deg 6.949
r_angle_other_deg 0.92
r_angle_refined_deg 1.547
r_bond_other_d 0.002
r_bond_refined_d 0.016
r_xyhbond_nbd_refined 0.165
r_symmetry_vdw_refined 0.074
r_symmetry_vdw_other 0.299
r_symmetry_hbond_refined 0.164
r_mcbond_it 0.791
r_mcangle_it 1.432
r_scbond_it 2.225
r_scangle_it 3.477
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
SCALEPACK data reduction
DENZO data collection