X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.17 α = 90
b = 83.71 β = 108.45
c = 56.01 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-3 mirrors 2004-11-08
Diffraction Radiation
Monochromator Protocol
Double Crystal Monochromator Si-111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.97945 APS 19-BM

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
2.15 50 98.7 0.118 0.118 -- 3.7 28301 28301 0.0 0.0 20.43
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)
2.15 2.23 95.7 0.395 0.395 1.8 3.1 2736

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 2.15 20.0 0.0 0.0 28251 28251 1431 96.93 -- 0.194 0.192 0.24 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 2.15 2.17 1527 74 1453 0.224 0.301 -- 71.22
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 16.469
Anisotropic B[1][1] 0.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.07
Anisotropic B[2][2] -0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.09
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.747
r_scbond_it 1.931
r_mcangle_it 1.471
r_mcbond_other 0.173
r_mcbond_it 0.986
r_symmetry_hbond_refined 0.179
r_symmetry_vdw_other 0.336
r_symmetry_vdw_refined 0.288
r_xyhbond_nbd_refined 0.19
r_nbtor_other 0.088
r_nbtor_refined 0.174
r_nbd_other 0.197
r_bond_refined_d 0.011
r_bond_other_d 0.002
r_angle_refined_deg 1.149
r_angle_other_deg 0.914
r_dihedral_angle_1_deg 4.853
r_dihedral_angle_2_deg 38.744
r_dihedral_angle_3_deg 16.386
r_dihedral_angle_4_deg 15.846
r_chiral_restr 0.071
r_gen_planes_refined 0.004
r_gen_planes_other 0.001
r_nbd_refined 0.209
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3978
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 134

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 2.000 data extraction
REFMAC5 version: 5.2.0019 refinement
HKL data processing