7NQB | pdb_00007nqb

X.ray structure of the oxaliplatin/beta-lactoglobulin adduct

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZSR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.2M KCl, 0.04M HEPES, 35% v/v pentaerythritol propoxylate

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.87	α = 90
b = 112.58	β = 117.637
c = 38.08	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	PIXEL	DECTRIS PILATUS 6M		2020-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.96	ELETTRA	11.2C

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	2.01	56.3	86.9	0.06	0.958	8.8	2.3		17918			19.3

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	2.01	56.3	92.4		0.152	0.939	3.9	1.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6ZSR	2.01	56.3	17379	772	97.635	0.216	0.2123	0.22	0.2845	0.28	24.961

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]
-0.105		-0.076	0.054		0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.574
r_dihedral_angle_3_deg	18.696
r_dihedral_angle_4_deg	8.786
r_dihedral_angle_1_deg	7.398
r_lrange_it	6.122
r_lrange_other	6.122
r_scangle_it	4.093
r_scangle_other	4.092
r_mcangle_it	3.337
r_mcangle_other	3.337
r_scbond_it	2.492
r_scbond_other	2.486
r_mcbond_it	2.071
r_mcbond_other	2.067
r_angle_refined_deg	1.532
r_angle_other_deg	1.174
r_nbd_other	0.239
r_symmetry_nbd_refined	0.222
r_nbd_refined	0.194
r_symmetry_nbd_other	0.192
r_symmetry_xyhbond_nbd_refined	0.178
r_xyhbond_nbd_refined	0.163
r_nbtor_refined	0.15
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2521
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	1

Software

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