4MCB | pdb_00004mcb

H.influenzae TrmD in complex with N-(4-{[(1H-IMIDAZOL-2-YLMETHYL)AMINO]METHYL}BENZYL)-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-5-CARBOXAMIDE

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	Protein at 10 mg/mL in the buffer: 20mM Tris pH 8.0, 150 mM NaCl, 10% Glycerol, 1mM DTT, 1mM EDTA. mixed 1:1 with well solution containing: 200 mM CaAcetate, 24% PEG 400, 100 mM Sodium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.158	α = 90
b = 74.158	β = 90
c = 119.288	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	140	CCD	RIGAKU SATURN 944+	multilayer monochrometer	2012-02-10		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.936	119.288	99.9	0.058	15.6	4.1	47863	47863			26.25

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	2.04	100		0.397	0.397	2	4	6968

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	1.94	38.8	47564	2405	99.87	0.1796	0.1782	0.18	0.2054	0.21	RANDOM	31.8175

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]
-0.677			-0.677		1.3541

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.1
t_omega_torsion	3.43
t_angle_deg	1.05
t_bond_d	0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.1
t_omega_torsion	3.43
t_angle_deg	1.05
t_bond_d	0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3477
Nucleic Acid Atoms
Solvent Atoms	575
Heterogen Atoms	76

Software

Software
Software Name	Purpose
SCALA	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
PROCESS	data reduction
AMoRE	phasing
BUSTER	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.