6YRV | pdb_00006yrv

Crystal structure of FAP after illumination at 100K

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YRU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	281	PEG 4000 25-40%, Na citrate 100 mM, spermidine 10mM

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.96	α = 90
b = 103.86	β = 90
c = 156.3	γ = 90

Symmetry
Space Group	I 2 2 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 EIGER X 4M		2018-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97372	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.94	86.5	100	0.106	0.116	0.998	11.62	6.585		54600			34.131

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	1.99	100		0.78	0.849	0.724	2.23	6.525

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6YRU	1.94	86	54459	2828	99.96	0.167	0.1651	0.17	0.2033	0.21	29.774

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]
0.984			0.631		-1.615

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.16
r_dihedral_angle_4_deg	16.441
r_dihedral_angle_3_deg	14.333
r_lrange_it	12.909
r_lrange_other	12.39
r_dihedral_angle_1_deg	7.441
r_scangle_it	5.02
r_scangle_other	5.02
r_scbond_it	3.416
r_scbond_other	3.416
r_mcangle_it	3.372
r_mcangle_other	3.372
r_mcbond_it	2.452
r_mcbond_other	2.45
r_angle_refined_deg	1.697
r_angle_other_deg	1.443
r_symmetry_nbd_refined	0.29
r_symmetry_xyhbond_nbd_refined	0.255
r_nbd_other	0.228
r_xyhbond_nbd_refined	0.222
r_nbd_refined	0.207
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.164
r_symmetry_xyhbond_nbd_other	0.091
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.082
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4267
Nucleic Acid Atoms
Solvent Atoms	524
Heterogen Atoms	93

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing