4WL9 | pdb_00004wl9

Time Resolved Serial Femtosecond Crystallography Captures High Resolution Intermediates of PYP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PHY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7	296	Microcrystals (~ 2 x 2 x 5 um^3) were formed by centrifugation in a spin filter.

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.9	α = 90
b = 66.9	β = 90
c = 40.8	γ = 120

Symmetry
Space Group	P 63

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	CS-PAD detector		2014-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.3784	SLAC LCLS	CXI

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Split (All)	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	1.6	16.73	100	0.065	12.4	1500		13500

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	2PHY	1.6	16.73	13500	654	97.62	0.1993	0.1978	0.2	0.2307	0.21	RANDOM	18.943

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]
-0.24	-0.12		-0.24		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.048
r_dihedral_angle_3_deg	15.668
r_dihedral_angle_4_deg	14.714
r_dihedral_angle_1_deg	6.133
r_scbond_it	3.297
r_mcangle_it	2.818
r_angle_refined_deg	2.097
r_mcbond_it	1.903
r_chiral_restr	0.161
r_bond_refined_d	0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.048
r_dihedral_angle_3_deg	15.668
r_dihedral_angle_4_deg	14.714
r_dihedral_angle_1_deg	6.133
r_scbond_it	3.297
r_mcangle_it	2.818
r_angle_refined_deg	2.097
r_mcbond_it	1.903
r_chiral_restr	0.161
r_bond_refined_d	0.02
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	976
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	11

Software

Software
Software Name	Purpose
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.