9ZXM | pdb_00009zxm

DDB1 delta with compound 6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FQD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M ammonium acetate, 0.1M Bis Tris pH 5.5-6.5, and 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.755	α = 90
b = 115.924	β = 90
c = 120.374	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 9M		2024-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.9201	NSLS-II	17-ID-1

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	2.195	33.11	99.16	0.1782	0.1919	0.07023	0.993	8.05	7.4		48885			28.06

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	2.2	2.22	95.28		0.7913	0.8588	0.3306	0.584	1.56	6.6

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.195	33.11	48865	2406	99.353	0.194	0.1911	0.1923	0.2461	0.248	RANDOM	38.786

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]
-0.574			1.957		-1.382

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.589
r_dihedral_angle_6_deg	13.962
r_lrange_it	8.821
r_lrange_other	8.819
r_dihedral_angle_2_deg	8.771
r_dihedral_angle_1_deg	7.626
r_scangle_it	6.04
r_scangle_other	6.04
r_mcangle_it	5.057
r_mcangle_other	5.056
r_scbond_it	3.738
r_scbond_other	3.737
r_mcbond_it	3.142
r_mcbond_other	3.141
r_angle_refined_deg	1.575
r_angle_other_deg	0.535
r_symmetry_xyhbond_nbd_refined	0.285
r_nbd_other	0.284
r_symmetry_nbd_refined	0.231
r_symmetry_nbd_other	0.213
r_nbd_refined	0.198
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.173
r_xyhbond_nbd_other	0.102
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.075
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6237
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing