Experiment: 1J7E

A Structural Basis for the Unique Binding Features of the Human Vitamin D-binding Protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J78

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	PEG 400, sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 20K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.977	α = 90
b = 131.977	β = 90
c = 73.42	γ = 90

Symmetry
Space Group	P 43

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	MARRESEARCH	toroidal mirror	2000-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	0.912	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.37	30	98.5	0.077	0.077	15.9	3.2		51580		-3	54.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.37	2.41	99.1		0.539	0.539	2.1	3.2	2503

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	1J78	2.55	29.51	39559	39559	1925	95.5	0.213	0.2125	0.263	0.2634	RANDOM	63.1

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]
-1.55			-1.55		3.1

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18.7
c_scangle_it	8.73
c_scbond_it	7.1
c_mcangle_it	5.6
c_mcbond_it	3.95
c_angle_deg	1.2
c_improper_angle_d	0.95
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6804
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	120

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing