X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 5
Temperature 293.0
Details 40% MPD, 0.1M sodium acetate trihydrate, pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.25 α = 90
b = 74.99 β = 90
c = 143.7 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 flat mirror 2003-06-01
Diffraction Radiation
Monochromator Protocol
single crystal Si(111) bent monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 -- SSRL BL11-1

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
1.65 35.93 95.9 -- 0.055 -- 4.7 40334 40334 -- -- 31.78
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)
1.65 1.74 78.8 -- 0.433 1.9 2.2 4754

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 1.65 35.93 -- -- -- 38297 2036 95.7 -- 0.15918 0.15768 0.18762 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 1.65 1.693 -- 121 2128 0.277 0.276 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 27.161
Anisotropic B[1][1] 0.67
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.98
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.32
r_scbond_it 2.522
r_mcangle_it 1.759
r_mcbond_it 0.959
r_symmetry_hbond_refined 0.26
r_symmetry_vdw_other 0.245
r_symmetry_vdw_refined 0.2
r_xyhbond_nbd_refined 0.236
r_nbtor_other 0.082
r_nbd_other 0.181
r_bond_refined_d 0.015
r_bond_other_d 0.001
r_angle_refined_deg 1.409
r_angle_other_deg 0.755
r_dihedral_angle_1_deg 5.544
r_dihedral_angle_2_deg 29.186
r_dihedral_angle_3_deg 14.127
r_dihedral_angle_4_deg 12.53
r_chiral_restr 0.083
r_gen_planes_refined 0.006
r_gen_planes_other 0.001
r_nbd_refined 0.21
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2090
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 295

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.1.9999 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.9999 refinement
MOLREP model building
SCALA(CCP4 version: 4.2) data reduction
MOSFLM data collection