1DZB | pdb_00001dzb

Crystal structure of phage library-derived single-chain Fv fragment 1F9 in complex with turkey egg-white lysozyme

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5		A SOLUTION OF SCFV FRAGMENT 1F9/TEL COMPLEX IN A 1:1 RATION IN 5 MM TRIS/HCL PH 7.5, 0.1 M NACL WAS MIXED WITH 10% PEG4000, 0.1 M AMMONIUMACETAT AND 0.05 M SODIUMACETATE BUFFER PH 5.0 AND EQUILIBRATED AGAINST 30% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.75	35.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.71	α = 90
b = 112.44	β = 97.67
c = 80	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	IMAGE PLATE	MARRESEARCH		1998-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31		EMBL/DESY, HAMBURG	X31

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	25	87.9	0.139	12.1	7.4		40240			27.683

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	2.07	75.5		0.196	3.77

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1JHL	2	20	40205	2011	87.9	0.225	0.23	0.306	0.3	RANDOM	32.3

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	28.1
p_staggered_tor	21.3
p_plane_restr	10.6
p_planar_tor	10.6
p_scangle_it	4.209
p_mcangle_it	4.025
p_scbond_it	2.923
p_mcbond_it	2.719
p_multtor_nbd	0.264
p_singtor_nbd	0.194
p_chiral_restr	0.166
p_xhyhbond_nbd	0.165
p_planar_d	0.083
p_angle_d	0.045
p_bond_d	0.015
p_angle_deg
p_hb_or_metal_coord
p_xyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5442
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing