Experiment: 3QHA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VPD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	MyavA.01379.a.A1 22.39 mg/ml, 20% PEG 6000, 0.1 M Hepes pH 7.0, 0.2M CaCl2, cryo-protectant 25% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.055	α = 90
b = 76.829	β = 90
c = 115.879	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315r			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97	ALS	5.0.1

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	2.25	50	100	0.105	7.3	7.2		29158

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	2.25	2.32	100		0.649		7.3	2415

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	MOLECULAR REPLACEMENT	THROUGHOUT	1VPD	2.25	50	28979	1475	99.5	0.2013	0.1995	0.21	0.2338	0.24	RANDOM	28.4089

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]
0.53			-1.22		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.036
r_dihedral_angle_4_deg	14.598
r_dihedral_angle_3_deg	13.206
r_dihedral_angle_1_deg	5.34
r_scangle_it	1.042
r_angle_refined_deg	0.916
r_angle_other_deg	0.841
r_scbond_it	0.598
r_mcangle_it	0.428
r_mcbond_it	0.224

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.036
r_dihedral_angle_4_deg	14.598
r_dihedral_angle_3_deg	13.206
r_dihedral_angle_1_deg	5.34
r_scangle_it	1.042
r_angle_refined_deg	0.916
r_angle_other_deg	0.841
r_scbond_it	0.598
r_mcangle_it	0.428
r_mcbond_it	0.224
r_chiral_restr	0.053
r_mcbond_other	0.026
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3968
Nucleic Acid Atoms
Solvent Atoms	284
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.