Experiment: 2O3C

Crystal structure of zebrafish Ape

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	290	AMMONIUM ACETATE, BIS-TRIS, PEG 3350, GLYCEROL, LEAD ACETATE, PH 5.5, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.66	α = 90
b = 117.78	β = 98.34
c = 85.84	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	CCD	NOIR-1		2005-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2		ALS	4.2.2

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	50	96.5	0.059	14.3	3.07	47731	46075			30.1

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)
	2.3	2.4	85.5		0.268	3.4	2.94

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 (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 1BIX	2.3	50	46050	2294	96.5	0.199	0.199	0.1995	0.236	0.2361	RANDOM	28.3

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]
-1.751		2.615	0.703		1.048

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.809
c_mcangle_it	2.242
c_scbond_it	1.936
c_angle_deg	1.38
c_mcbond_it	1.353
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6644
Nucleic Acid Atoms
Solvent Atoms	362
Heterogen Atoms	3

Software

Software
Software Name	Purpose
MOLREP	phasing
CNS	refinement
JBluIce-EPICS	data collection
d*TREK	data reduction
d*TREK	data scaling