8REL | pdb_00008rel

Fab of an anti-PvAMA1 monoclonal antibody

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YHQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		290	Crystals of Fab8.1.1 were obtained by mixing 1 micro-L of protein and 1 micro-L of reservoir containing 24% PEG 4000, 80 mM sodium acetate pH 4.6 and 0.16 M ammonium acetate. The final protein concentration was 3.6 mg/ml. Cryo-protecting buffer for FabF8.1.1 consisted of the crystallisation buffer where PEG was increased to 30% added with 15% of glycerol (v/v).

Crystal Properties
Matthews coefficient	Solvent content
1.95	37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.49	α = 90
b = 61.52	β = 97.49
c = 116.99	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	ADSC QUANTUM 210r		2006-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9340	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.1	46.02	94.8	0.139	0.162	0.083	0.991	7.7	3.8		41875

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.21	74.7		0.608	0.713	0.369	0.503	2.1	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.1	42.24	40631	1231	94.57	0.20206	0.20035	0.2057	0.25461	0.2546	RANDOM	30.766

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]
-0.94		0.03	0.71		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.85
r_dihedral_angle_1_deg	6.846
r_long_range_B_refined	5.095
r_dihedral_angle_2_deg	5.069
r_long_range_B_other	5.018
r_scangle_other	2.587
r_mcangle_it	2.419
r_mcangle_other	2.419
r_scbond_it	1.549
r_scbond_other	1.547
r_mcbond_it	1.437
r_mcbond_other	1.436
r_angle_refined_deg	1.065
r_angle_other_deg	0.386
r_chiral_restr	0.052
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6344
Nucleic Acid Atoms
Solvent Atoms	438
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing