Experiment: 3MF7

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MF8	PDB entry 3MF8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	4.6	298	three micro liter of 15.6mg/mL cis-CaaD protein sample mixed with three micro liter crystallization solution: 0.125 M CaCl2, 0.07 M sodium acetate buffer, 12.5% isopropanol, hanging drop, temperature 298K, pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.783	α = 90
b = 96.783	β = 90
c = 96.783	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS		2005-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	1.62	50	98.9	0.063	24	4.6		19123

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)
	1.62	1.68	91.2		0.241		4.4	1751

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3MF8	1.65	50	17952	935	98.19	0.188	0.186	0.222	RANDOM	9.866

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.679
r_dihedral_angle_4_deg	19.029
r_dihedral_angle_3_deg	14.534
r_dihedral_angle_1_deg	5.288
r_scangle_it	3.38
r_scbond_it	2.281
r_angle_refined_deg	1.289
r_mcangle_it	1.282
r_mcbond_it	0.864
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.679
r_dihedral_angle_4_deg	19.029
r_dihedral_angle_3_deg	14.534
r_dihedral_angle_1_deg	5.288
r_scangle_it	3.38
r_scbond_it	2.281
r_angle_refined_deg	1.289
r_mcangle_it	1.282
r_mcbond_it	0.864
r_nbtor_refined	0.306
r_nbd_refined	0.27
r_symmetry_vdw_refined	0.204
r_symmetry_hbond_refined	0.176
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	923
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms

Software

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

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.