Experiment: 1IMV

2.85 A crystal structure of PEDF

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	293	0.2M ammonium fluoride, 20% PEG 3350, pH 6.20, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 176.174	α = 90
b = 62.514	β = 90
c = 45.406	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	RIGAKU RAXIS IIC	focusing mirrors	2001-04-06	M	SINGLE WAVELENGTH
2	1	x-ray	298	IMAGE PLATE	RIGAKU RAXIS IIC	focusing mirrors	2001-04-08	M	SINGLE WAVELENGTH
3	1	x-ray	298	IMAGE PLATE	RIGAKU RAXIS IIC	focusing mirrors	2001-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418
2	ROTATING ANODE	RIGAKU RU200	1.5418
3	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
1,2,3	2.85	36.74	92.1	0.127	8.5	12.7	11214	11214			45.2

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)
1,2,3	2.85	3.03	65.4		0.37		3	1166

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	PDB entry 1QLP	2.85	36.74	11241	11241	1167	91.2	0.188	0.1908	0.227	0.2293	RANDOM	31.4

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]
-3.92			7.44		-3.52

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.1
c_scangle_it	2.98
c_mcangle_it	2.19
c_scbond_it	1.84
c_angle_deg	1.3
c_mcbond_it	1.25
c_improper_angle_d	0.79
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2923
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	14

Software

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