Experiment: 1J78

Crystallographic analysis of the human vitamin D binding protein

X-RAY DIFFRACTION

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	60.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.248	α = 90
b = 132.248	β = 90
c = 73.179	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	Bent mirror	1999-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.9116	EMBL/DESY, HAMBURG	X11

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	2.31	30	99.2	0.031	0.031	22.7	3.4	55933	55444		-3	50.6

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)
	2.31	2.35	99.6		0.209	0.209	5.2	3.4	2766

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	COMBINED MAD AND MIRAS	THROUGHOUT	2.31	29.38	55159	55159	2221	99.2	0.22	0.2201	0.252	0.2516	RANDOM	60.5

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]
3.24			3.24		-6.49

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18.8
c_scangle_it	8.43
c_scbond_it	6.72
c_mcangle_it	5.61
c_mcbond_it	4.09
c_angle_deg	1.2
c_improper_angle_d	0.89
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6749
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	89

Software

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