9R6W | pdb_00009r6w

CHAP domain of Pneumococcal Endopeptidase PcsB

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	100mM Sodium citrate(pH 5.6), 500mM NaCl, 4 % v/v Polyethyleneimine

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.28	α = 90
b = 117.38	β = 90
c = 47.69	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS EIGER2 XE 9M		2022-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	45	100	0.83	19.5	13.3		52851

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73			0.252

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.7	44.222	52851	2634	99.966	0.173	0.1719	0.1833	0.1941	0.1994	18.687

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			-0.003		0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.626
r_dihedral_angle_4_deg	12.94
r_dihedral_angle_3_deg	11.697
r_dihedral_angle_1_deg	6.482
r_lrange_it	4.48
r_lrange_other	4.448
r_scangle_it	3.692
r_scangle_other	3.691
r_scbond_it	2.637
r_scbond_other	2.636
r_mcangle_it	2.426
r_mcangle_other	2.426
r_angle_refined_deg	1.745
r_mcbond_it	1.728
r_mcbond_other	1.712
r_angle_other_deg	1.622
r_nbd_other	0.255
r_nbd_refined	0.214
r_symmetry_nbd_refined	0.2
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.186
r_symmetry_xyhbond_nbd_refined	0.147
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3282
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
REFMAC	phasing