Experiment: 1MA9

Crystal structure of the complex of human vitamin D binding protein and rabbit muscle actin

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	277	PEG 8000, magnesium acetate, sodium cacodylate, glycerol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.44	α = 90
b = 74.9	β = 110.19
c = 88.02	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	IMAGE PLATE	MARRESEARCH	premirror, triangular monochromator, bent mirror	2000-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.8423	EMBL/DESY, HAMBURG	BW7B

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	2.4	20	93.3	0.042	0.042	12.2	2.9	35664	33202		-3	36.3

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)
	2.4	2.44	93.9		0.25	0.25	1.8	2.6	1633

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-Factor (All)	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 ENTRIES 1ATN, 1J78	2.4	19.91	32191	32191	2455	90.3	0.2033	0.2033	0.2	0.1965	0.25	0.2459	RANDOM	52.2

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]
2.44		4.77	-7.28		4.84

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.9
c_scangle_it	8.97
c_scbond_it	7.47
c_mcangle_it	2.3
c_mcbond_it	1.37
c_angle_deg	1.2
c_improper_angle_d	0.82
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6151
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms	32

Software

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