X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Small Tubes
pH 6.7
Temperature 287.0
Details BES, EDTA, pH 6.7, SMALL TUBES, temperature 287K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.71 α = 90
b = 128.71 β = 90
c = 117.44 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV MSC/Yale double Mirrors 1999-02-11
Diffraction Radiation
Monochromator Protocol
Graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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
2.5 24.69 91.3 -- 0.069 -- 3.7 31719 31719 0.0 -3.0 48.1
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)
2.5 2.54 93.7 -- 0.485 3.3 3.6 2352

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
FOURIER SYNTHESIS 2.5 24.69 -- 0.0 30080 30080 1613 91.45 0.19242 0.19242 0.18972 0.24276 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 2.5 2.565 2352 122 2230 0.268 0.331 -- 93.89
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 53.861
Anisotropic B[1][1] 0.71
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.71
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.42
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 1.292
r_symmetry_vdw_refined 0.139
r_dihedral_angle_1_deg 5.604
r_bond_refined_d 0.009
r_gen_planes_refined 0.004
r_nbtor_refined 0.307
r_mcangle_it 1.095
r_angle_refined_deg 1.199
r_mcbond_it 0.613
r_dihedral_angle_2_deg 35.581
r_nbd_refined 0.201
r_chiral_restr 0.084
r_dihedral_angle_4_deg 18.284
r_symmetry_hbond_refined 0.237
r_scangle_it 2.151
r_dihedral_angle_3_deg 17.733
r_xyhbond_nbd_refined 0.136
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.209
Luzzati ESD (R-Free Set) 0.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6553
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 87

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
DENZO data reduction
SCALEPACK data scaling