X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 298.0
Details 0.05 M potassium phosphate, 26% Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.32 α = 90
b = 136.32 β = 90
c = 121.52 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ confocal 2004-01-17
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 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
2.25 96.23 98.9 0.101 -- -- 3.0 27570 27220 0.0 0.0 42.0
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)
2.25 2.3 93.1 0.751 -- 1.3 -- --

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 2.25 96.23 -- -- 27220 25853 1367 98.87 -- 0.16288 0.15917 0.23416 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 2.247 2.306 1726 93 1721 0.273 0.373 -- 91.16
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 36.128
Anisotropic B[1][1] -0.39
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.79
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.257
r_scbond_it 2.818
r_mcangle_it 2.071
r_mcbond_it 1.251
r_nbd_refined 0.213
r_gen_planes_refined 0.007
r_chiral_restr 0.114
r_dihedral_angle_4_deg 14.975
r_dihedral_angle_3_deg 17.251
r_dihedral_angle_2_deg 33.78
r_dihedral_angle_1_deg 7.359
r_angle_refined_deg 1.774
r_bond_refined_d 0.019
r_nbtor_refined 0.311
r_xyhbond_nbd_refined 0.172
r_metal_ion_refined 0.318
r_symmetry_vdw_refined 0.2
r_symmetry_hbond_refined 0.179
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4658
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 353

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
Molrep Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
Molrep model building
CrystalClear data collection