9GWZ | pdb_00009gwz

Crystal structure of 23ME-00610 Fab

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	MPD 50.0% v/v; NH4H2PO4 0.20M; Tris-HCL 0.10M pH 8.50

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 225.274	α = 90
b = 67.447	β = 101.71
c = 136.88	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	100	PIXEL	DECTRIS EIGER2 S 16M		2022-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.12	95.167	97.8	0.159	0.989	7.8	7.4		112044

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.12	2.157			1.178	0.46

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	2.12	67.106	111756	5592	97.543	0.22	0.2182	0.2221	0.2562	0.2616	43.299

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]
3.704		-2.166	-1.222		-1.459

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.298
r_dihedral_angle_4_deg	18.149
r_dihedral_angle_3_deg	12.995
r_dihedral_angle_1_deg	7.572
r_lrange_it	5.634
r_lrange_other	5.598
r_scangle_it	3.26
r_scangle_other	3.26
r_mcangle_it	3.174
r_mcangle_other	3.174
r_scbond_it	2.022
r_scbond_other	2.022
r_mcbond_it	1.967
r_mcbond_other	1.967
r_angle_refined_deg	1.391
r_angle_other_deg	1.105
r_ext_dist_refined_d	0.599
r_symmetry_nbd_other	0.151
r_nbd_other	0.151
r_nbd_refined	0.147
r_nbtor_refined	0.141
r_xyhbond_nbd_refined	0.135
r_symmetry_xyhbond_nbd_refined	0.13
r_symmetry_nbd_refined	0.075
r_symmetry_nbtor_other	0.067
r_chiral_restr	0.048
r_ncsr_local_group_8	0.031
r_ncsr_local_group_2	0.03
r_ncsr_local_group_11	0.03
r_ncsr_local_group_1	0.027
r_ncsr_local_group_7	0.025
r_ncsr_local_group_3	0.023
r_ncsr_local_group_4	0.019
r_ncsr_local_group_6	0.019
r_ncsr_local_group_9	0.017
r_ncsr_local_group_5	0.015
r_ncsr_local_group_10	0.015
r_ncsr_local_group_12	0.015
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13091
Nucleic Acid Atoms
Solvent Atoms	749
Heterogen Atoms	61

Software

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