8CCR | pdb_00008ccr

Crystal structure of the T19D mutant of the de novo diheme binding 4D2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7AH0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Crystallisation buffer: 2.1 M DL-malic acid, Purification buffer: 20 mM CHES, 100mM KCl, pH 8.6

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.093	α = 90
b = 81.093	β = 90
c = 58.585	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	193	PIXEL	DECTRIS EIGER2 X 16M		2021-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.1	40.58	100	0.102	0.105	15.4	21.2		8376

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16	100		0.367	0.376	3.8	21.4

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 (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	2.1	40.55	7531	840	99.99	0.20292	0.1995	0.21	0.23259	0.23	RANDOM	44.276

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]
0.07	0.03		0.07		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.349
r_dihedral_angle_4_deg	28.746
r_dihedral_angle_3_deg	17.389
r_long_range_B_other	8.016
r_long_range_B_refined	8
r_scangle_other	6.248
r_dihedral_angle_1_deg	5.12
r_mcangle_it	4.884
r_mcangle_other	4.884
r_scbond_it	4.161
r_scbond_other	4.133
r_mcbond_it	2.978
r_mcbond_other	2.97
r_angle_other_deg	2.578
r_angle_refined_deg	2.561
r_chiral_restr	0.238
r_gen_planes_other	0.067
r_bond_other_d	0.034
r_gen_planes_refined	0.029
r_bond_refined_d	0.022
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	837
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	96

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data scaling
DIALS	data reduction
MOLREP	phasing