2Y36 | pdb_00002y36

Crystal structure analysis of the anti-(4-hydroxy-3-nitrophenyl)- acetyl murine germline antibody BBE6.12H3 Fab fragment in complex with a phage display derived dodecapeptide DLWTTAIPTIPS

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		NATIVE FAB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.1		0.05M TRIS HCL, 0.025% SODIUM AZIDE, PEG 3350., pH 7.1

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.01	α = 90
b = 63.62	β = 90.4
c = 113.38	γ = 90

Symmetry
Space Group	C 1 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	287	CCD	MARMOSAIC 225 mm CCD	BENT COLLIMATING MIRROR AND TOROID	2009-08-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	50	100	0.07	11.3	5.1		11098			28.3

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	8.5	100		0.28	4.1	5.1

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	NATIVE FAB	2.7	50	9995	1081	90.1	0.2305	0.2305	0.23	0.2477	0.28	RANDOM	42.4

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]
-12.165		-1.132	26.388		-14.223

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	28.5
c_angle_deg	1.96434
c_improper_angle_d	1.3
c_bond_d	0.009918
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3294
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing