8RMO | pdb_00008rmo

Crystal structure of anti-FLAG M2 Fab fragment bound to FLAG-tag peptide epitope

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7BG1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.1 M TRIS 8 pH, 20 %w/v PEG 6K, 0.2 M NH4Cl

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.432	α = 90
b = 134.621	β = 90
c = 41.798	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 9M		2023-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.6199	Diamond	I24

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	1.163	73.326	95.71	0.151	0.153	0.026	0.9989	16.525	36.99		123223

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	1.163	1.245	71.98		6.867	7.008	1.388	0.6095	1.526

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.163	73.326	120660	6057	71.122	0.159	0.1575	0.16	0.1855	0.19	25.358

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]
-4.286			2.619		1.667

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.793
r_dihedral_angle_2_deg	16.027
r_dihedral_angle_3_deg	12.419
r_dihedral_angle_1_deg	7.234
r_lrange_it	4.637
r_rigid_bond_restr	4.235
r_lrange_other	4.137
r_scangle_it	2.824
r_scangle_other	2.824
r_mcangle_it	2.688
r_mcangle_other	2.687
r_scbond_it	2.026
r_scbond_other	2.025
r_mcbond_it	1.901
r_mcbond_other	1.892
r_angle_refined_deg	1.564
r_chiral_restr_other	1.537
r_angle_other_deg	1.066
r_nbd_refined	0.221
r_symmetry_nbd_other	0.205
r_xyhbond_nbd_refined	0.187
r_nbd_other	0.175
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.151
r_symmetry_nbd_refined	0.132
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.087
r_gen_planes_other	0.012
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3257
Nucleic Acid Atoms
Solvent Atoms	517
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing