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 = 55.67 α = 90
b = 77.96 β = 109.05
c = 58 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 ADSC QUANTUM 315 Rosenbaum-Rock vertical focusing mirror 2004-11-08
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock high-resolution double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID

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
1.85 50 97.0 0.049 0.049 -- 3.1 38560 38560 0.0 0.0 26.39
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)
1.85 1.901 76.29 0.367 0.367 1.79 2.4 2204

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 1.85 19.89 0.0 0.0 38516 38516 1935 96.85 -- 0.214 0.211 0.264 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 1.85 1.901 2204 110 2094 0.351 0.428 -- 76.29
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 48.196
Anisotropic B[1][1] 0.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] -0.18
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 11.112
r_scbond_it 8.369
r_mcangle_it 4.979
r_mcbond_it 3.646
r_symmetry_hbond_refined 0.194
r_bond_refined_d 0.01
r_angle_refined_deg 1.278
r_dihedral_angle_1_deg 4.814
r_dihedral_angle_2_deg 39.498
r_dihedral_angle_3_deg 17.891
r_dihedral_angle_4_deg 21.92
r_chiral_restr 0.086
r_gen_planes_refined 0.005
r_nbd_refined 0.244
r_nbtor_refined 0.316
r_xyhbond_nbd_refined 0.208
r_symmetry_vdw_refined 0.289
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3882
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 70

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 2.000 data extraction
REFMAC5 version: 5.2.0005 refinement