4S1D | pdb_00004s1d

Structure of IgG1 Fab fragment in complex with Biotincytidinamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		unpublished in house Fab fragment structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	0.15M ammonium sulfate, 0.1M MES, 15%PEG 4000, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.094	α = 90
b = 119.62	β = 117.15
c = 96.181	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	110	PIXEL	PSI PILATUS 6M		2011-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1	SLS	X10SA

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	2.35	119	99.9	0.057	10.29	3.47	74713	74645

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.4	99.9		0.65		3.53	3658

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	unpublished in house Fab fragment structure	2.5	119	62797	58977	3132	99.91	0.22799	0.22547	0.23	0.27446	0.27	RANDOM	78.96

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]
-1.24		4.17	-2.72		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.185
r_dihedral_angle_4_deg	14.784
r_dihedral_angle_3_deg	13.842
r_dihedral_angle_1_deg	5.638
r_long_range_B_refined	5.383
r_long_range_B_other	5.342
r_mcangle_it	1.929
r_mcangle_other	1.929
r_scangle_other	1.555
r_mcbond_it	1.109
r_mcbond_other	1.108
r_angle_refined_deg	0.994
r_scbond_it	0.966
r_scbond_other	0.887
r_angle_other_deg	0.641
r_chiral_restr	0.058
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13109
Nucleic Acid Atoms
Solvent Atoms	336
Heterogen Atoms	105

Software

Software
Software Name	Purpose
DA+	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SADABS	data scaling