8APW | pdb_00008apw

Crystal Structure of H. influenzae TrmD in complex with Compound 30

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YVH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	20% PEG3350 0.1 M HEPES, pH 7.5 0.1 M potassium citrate tribasic

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.367	α = 90
b = 94.367	β = 90
c = 178.289	γ = 120

Symmetry
Space Group	H 3 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	CCD	RIGAKU SATURN 944+		2020-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.8	47.228	99.8	0.07	0.078	0.033	0.999	26.1	10.4		28538

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	1.8	1.84			0.019	0.021	0.01	0.999		8.2

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	4YVH	1.8	47.228	28536	2754	99.658	0.171	0.1677	0.18	0.2027	0.21	25.033

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]
					0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.476
r_dihedral_angle_3_deg	14.87
r_dihedral_angle_4_deg	12.605
r_lrange_it	8.979
r_lrange_other	8.779
r_scangle_it	7.212
r_scangle_other	7.21
r_dihedral_angle_1_deg	6.648
r_scbond_it	5.419
r_scbond_other	5.416
r_mcangle_it	5.161
r_mcangle_other	5.159
r_dihedral_angle_other_2_deg	5.126
r_mcbond_it	3.914
r_mcbond_other	3.912
r_angle_refined_deg	2.445
r_angle_other_deg	1.593
r_xyhbond_nbd_refined	0.418
r_chiral_restr_other	0.293
r_symmetry_xyhbond_nbd_refined	0.275
r_nbd_other	0.264
r_nbd_refined	0.242
r_symmetry_nbd_other	0.21
r_nbtor_refined	0.178
r_symmetry_nbd_refined	0.155
r_chiral_restr	0.151
r_symmetry_nbtor_other	0.093
r_symmetry_xyhbond_nbd_other	0.038
r_bond_refined_d	0.026
r_gen_planes_refined	0.018
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1965
Nucleic Acid Atoms
Solvent Atoms	317
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
StructureStudio	data collection
PHASER	phasing