1QX2

X-ray Structure of Calcium-loaded Calbindomodulin (A Calbindin D9k Re-engineered to Undergo a Conformational Opening) at 1.44 A Resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291PEG 550 MME, MES, zinc sulfate, Tris-HCl, sodium chloride, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.8934.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.54α = 90
b = 62.174β = 90
c = 69.463γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2003-03-17MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0000, 1.2818, 1.2823, 1.2703APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.445094.70.07520.2224352243519.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.441.4958.40.1646.11349

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.4428.4212452124511641000.158250.158250.156350.19358RANDOM10.795
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.703
r_scangle_it3.665
r_sphericity_free2.388
r_scbond_it2.187
r_angle_refined_deg1.465
r_mcangle_it1.456
r_sphericity_bonded1.454
r_angle_other_deg1.443
r_rigid_bond_restr1.108
r_mcbond_it0.832
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.703
r_scangle_it3.665
r_sphericity_free2.388
r_scbond_it2.187
r_angle_refined_deg1.465
r_mcangle_it1.456
r_sphericity_bonded1.454
r_angle_other_deg1.443
r_rigid_bond_restr1.108
r_mcbond_it0.832
r_nbd_refined0.237
r_nbd_other0.221
r_symmetry_vdw_other0.195
r_symmetry_vdw_refined0.188
r_symmetry_hbond_refined0.156
r_xyhbond_nbd_refined0.138
r_nbtor_other0.094
r_chiral_restr0.071
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1173
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing