8TV8 | pdb_00008tv8

Crystal structure of nontypeable Haemophilus influenzae SapA

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.4	295	0.1 M Tris pH 9.4, 1.5 M ammonium phosphate, 0.18 M sodium thiocyanate

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.755	α = 90
b = 119.755	β = 90
c = 129.585	γ = 90

Symmetry
Space Group	P 41 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	CCD	RAYONIX MX-300		2016-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.978560	APS	21-ID-G

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	2.25	44.014	99.9	0.089	0.091	0.021	0.998	16.1	19.2		45307

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	2.25	2.32		100	0.718	0.737	0.165	0.939		19.9

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	THROUGHOUT	2.25	44.014	45239	2322	99.868	0.198	0.197	0.2	0.225	0.23	54.689

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]
-0.113			-0.113		0.227

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.684
r_dihedral_angle_3_deg	15.632
r_dihedral_angle_2_deg	15.333
r_lrange_it	10.779
r_lrange_other	10.778
r_scangle_it	8.657
r_scangle_other	8.656
r_dihedral_angle_1_deg	7.093
r_mcangle_it	7.057
r_mcangle_other	7.056
r_scbond_it	6.101
r_scbond_other	6.1
r_mcbond_other	5.399
r_mcbond_it	5.398
r_angle_refined_deg	1.691
r_angle_other_deg	0.622
r_nbd_refined	0.216
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.173
r_symmetry_nbd_refined	0.166
r_nbd_other	0.145
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.076
r_symmetry_xyhbond_nbd_refined	0.075
r_symmetry_xyhbond_nbd_other	0.022
r_bond_other_d	0.012
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4152
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
BALBES	phasing
ARP/wARP	model building
PDB_EXTRACT	data extraction