Experiment: 4KUZ

Crystal structure of anti-emmprin antibody 4A5 Fab in trigonal form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IL1	PDB ENTRIES 1IL1 AND 1IGJ
experimental model	PDB	1IGJ	PDB ENTRIES 1IL1 AND 1IGJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	293	0.1 M CHES, pH 9.5, 2.0 M ammonium sulfate, 5% isopropanol, cryoprotectant: mother liquor + 25% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.6	73.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.43	α = 90
b = 126.43	β = 90
c = 97.15	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	RIGAKU SATURN 944	VARIMAX HF	2008-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	2.7	30	99.3	0.103	20.7	11	24553	24553		-3	34.8

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	2.7	2.8	93		0.477	4	6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRIES 1IL1 AND 1IGJ	2.7	29.2	1.34	23389	24553	2014	99.38	0.2332	0.2302	0.2282	0.2684	0.2689	57.1

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]
1.42	0.71		1.42		-2.13

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.937
f_angle_d	1.223
f_chiral_restr	0.076
f_bond_d	0.009
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3321
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	20

Software

Software
Software Name	Purpose
PHENIX	refinement
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling
CrystalClear	data collection