2O9J | pdb_00002o9j

Crystal structure of calcium atpase with bound magnesium fluoride and cyclopiazonic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WPG	pdb entry 1WPG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	284	8% PEG 3350, 21% glycerol, 20mM MgCl2, 0.1mM EGTA, 20 mM MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 284K

Crystal Properties
Matthews coefficient	Solvent content
3.83	67.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.383	α = 90
b = 69.875	β = 107.1
c = 143.411	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	ADSC QUANTUM 315		2005-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 12.3.1		ALS	12.3.1

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	2.65	30	99.7	0.063	15	4		48660		2

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	2.65	2.74	100		0.511		4	4855

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1WPG	2.65	29.1	48429	2421	99.67	0.248	0.246	0.24	0.287	0.24	RANDOM	83.564

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]
-0.21		-0.24	-0.06		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.344
r_dihedral_angle_3_deg	16.434
r_dihedral_angle_4_deg	16.042
r_dihedral_angle_1_deg	4.417
r_scangle_it	1.55
r_angle_refined_deg	1.28
r_scbond_it	0.886
r_mcangle_it	0.831
r_mcbond_it	0.447
r_nbtor_refined	0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.344
r_dihedral_angle_3_deg	16.434
r_dihedral_angle_4_deg	16.042
r_dihedral_angle_1_deg	4.417
r_scangle_it	1.55
r_angle_refined_deg	1.28
r_scbond_it	0.886
r_mcangle_it	0.831
r_mcbond_it	0.447
r_nbtor_refined	0.323
r_symmetry_hbond_refined	0.263
r_nbd_refined	0.225
r_symmetry_vdw_refined	0.216
r_xyhbond_nbd_refined	0.194
r_metal_ion_refined	0.114
r_chiral_restr	0.076
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7562
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	32

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.