4MX9 | pdb_00004mx9

CDPK1 from Neospora caninum in complex with inhibitor UW1294

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4M97	PDB ENTRY 4M97

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	protein solution: 25 mM HEPES pH 7.0, 0.5 M NaCl, 5% glycerol, 5 mM DTT, 20 mM EGTA, 3mg/ml protein, 0.2 mM UW1294, 1% DMSO; crystallization buffer: 30% PEG 3350, 0.2 M ammonium citrate, 0.1 M BisTris pH 5.3, 5 mM DTT, vapor diffusion, sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.38	α = 90
b = 73.141	β = 99.84
c = 66.27	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M		2013-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97939	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.1	65.3	91.7	0.264	4.5	2.6		7664

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.31	92.6		0.011	1.5	2.6	1404

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 4M97	3.1	48.76	7197	336	85.74	0.2502	0.2491	0.2743	0.2798	RANDOM	78.5996

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]
2.02		2.75	2.3		-4.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.618
r_dihedral_angle_3_deg	16.48
r_dihedral_angle_4_deg	16.01
r_dihedral_angle_1_deg	5.437
r_mcangle_it	3.371
r_mcbond_it	1.893
r_mcbond_other	1.893
r_angle_refined_deg	1.438
r_angle_other_deg	0.934
r_chiral_restr	0.073
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3670
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	31

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction