4CGK | pdb_00004cgk

Crystal structure of the essential protein PcsB from Streptococcus pneumoniae

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		CRYSTALS GREW IN 2UL DROPLETS FORMED BY MIXING 1 UL OF PROTEIN SOLUTION AT 10 MG ML-1 (BUFFERED IN 20 MM TRIS-HCL PH 7.5) AND 1 UL L OF PRECIPITANT SOLUTION FORMED BY 12% (V/V) POLYETHYLENGLYCOL 4000, 0.1M HEPES PH 7.5, 0.2M MAGNESIUM ACETATE IN 1:1 VOLUME RATIO

Crystal Properties
Matthews coefficient	Solvent content
3.9	68.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.815	α = 90
b = 125.815	β = 90
c = 126.637	γ = 120

Symmetry
Space Group	P 31 2 1

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 PILATUS 6M			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.55	44.63	99.9	0.08	11.9	10.6		38172		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.66	99.8		0.64	2.9	11

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	NONE	2.55	44.63	36230	1907	99.85	0.23933	0.23761	0.24	0.27173	0.27	RANDOM	77.41

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]
36.7			36.7		-73.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.928
r_dihedral_angle_3_deg	15.512
r_dihedral_angle_4_deg	13.793
r_dihedral_angle_1_deg	4.232
r_mcangle_it	2.642
r_angle_other_deg	1.709
r_mcbond_it	1.447
r_mcbond_other	1.447
r_scbond_it	1.124
r_angle_refined_deg	0.834
r_chiral_restr	0.047
r_bond_refined_d	0.005
r_bond_other_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5222
Nucleic Acid Atoms
Solvent Atoms	448
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
SHELX	phasing