X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.3
Temperature 277.0
Details PEG 4000, calcium acetate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.45 α = 90
b = 77.04 β = 107.63
c = 111.01 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2004-12-03
Diffraction Radiation
Monochromator Protocol
Double crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 0.9537 ALS 8.2.2

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
2.2 50 -- -- 0.075 -- 2.4 -- 48471 0.0 0.0 --
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)
2.2 2.25 86.9 -- 0.37 2.0 -- --

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 2.2 39.68 -- -- 44014 44014 1414 93.72 -- 0.24321 0.24156 0.29368 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 2.203 2.26 -- 88 2983 0.337 0.438 -- 86.34
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 71.352
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.02
Anisotropic B[2][2] -0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.07
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.552
r_scbond_it 1.757
r_mcangle_it 1.135
r_mcbond_it 0.737
r_nbd_refined 0.232
r_gen_planes_refined 0.002
r_chiral_restr 0.149
r_dihedral_angle_4_deg 22.531
r_dihedral_angle_3_deg 17.989
r_dihedral_angle_2_deg 33.895
r_dihedral_angle_1_deg 5.792
r_angle_refined_deg 1.848
r_bond_refined_d 0.015
r_nbtor_refined 0.313
r_xyhbond_nbd_refined 0.179
r_symmetry_vdw_refined 0.199
r_symmetry_hbond_refined 0.18
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.45
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5911
Nucleic Acid Atoms 0
Heterogen Atoms 214
Solvent Atoms 165

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
CCP4 (TRUNCATE) Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0003 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0003 refinement