1YR5

1.7-A structure of calmodulin bound to a peptide from DAP kinase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WRZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	295	PEG 8000, sodium acetate, calcium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.07	α = 90
b = 33.71	β = 111.16
c = 75.89	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH		2005-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.938	EMBL/DESY, HAMBURG	BW7A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	20	96.8	0.056	20.1	4.6	16769	16769	-3	-3	28

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.75	94.5		0.52	2.6	3.5	1362

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1WRZ	1.7	20	-3	16768	16768	846	96.21	0.20286	0.20286	0.19999	0.21	0.25707	0.26	RANDOM	9.375

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]
1.65		0.81	-0.87		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.495
r_dihedral_angle_4_deg	18.557
r_dihedral_angle_3_deg	17.418
r_dihedral_angle_1_deg	5.915
r_scangle_it	3.596
r_scbond_it	2.547
r_angle_other_deg	2.026
r_mcangle_it	1.797
r_angle_refined_deg	1.442
r_mcbond_it	1.408
r_symmetry_vdw_other	0.255
r_nbd_refined	0.229
r_nbd_other	0.205
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.173
r_mcbond_other	0.165
r_symmetry_vdw_refined	0.154
r_symmetry_hbond_refined	0.142
r_chiral_restr	0.091
r_nbtor_other	0.082
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1320
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing