3AAZ

Crystal structure of the humanized recombinant Fab fragment of a murine; antibody

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BAE	PDB ENTRY 3BAE, 1UM5, 8FAB
experimental model	PDB	1UM5	PDB ENTRY 3BAE, 1UM5, 8FAB
experimental model	PDB	8FAB	PDB ENTRY 3BAE, 1UM5, 8FAB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	298	20% PEG 3350, 0.2M sodium sulfate, 0.2M lithium citrate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.732	α = 90
b = 106.732	β = 90
c = 90.867	γ = 120

Symmetry
Space Group	P 31

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	ADSC QUANTUM 210r	mirrors	2009-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9566	Australian Synchrotron	MX1

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	2.2	46.03	92.5	0.09	16.5	3.7	51677	51677		2	26.511

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	2.2	2.26	64.1		0.43	2	3	2641

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3BAE, 1UM5, 8FAB	2.2	46.03	51677	51677	2734	92.55	0.21247	0.20923	0.27134	RANDOM	28.225

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]
4.29	2.14		4.29		-6.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.565
r_dihedral_angle_3_deg	19.223
r_dihedral_angle_4_deg	17.965
r_dihedral_angle_1_deg	7.744
r_scangle_it	3.077
r_scbond_it	2.1
r_angle_refined_deg	1.742
r_mcangle_it	1.199
r_mcbond_it	0.664
r_chiral_restr	0.117
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7018
Nucleic Acid Atoms
Solvent Atoms	383
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling