8VQG | pdb_00008vqg

X-ray crystal structure of Can f 1

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8EPU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	1.5 M sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.494	α = 90
b = 109.16	β = 90
c = 127.764	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS EIGER2 XE 16M		2022-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.5	40	99.9	0.09	0.09	0.097	0.036	0.996	24.3	7.2		20197

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.59	99.3		0.623	0.623	0.676	0.258	0.811	2.3	6.2

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	PDB entry 8EPU	2.55	36.015	19814	1009	99.834	0.224	0.2218	0.2234	0.2596	0.2619	60.723

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]
-0.977			3.23		-2.254

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.981
r_dihedral_angle_3_deg	11.629
r_dihedral_angle_1_deg	7.229
r_lrange_it	3.747
r_lrange_other	3.708
r_mcangle_it	2.191
r_mcangle_other	2.191
r_dihedral_angle_2_deg	2.129
r_scangle_it	1.76
r_scangle_other	1.759
r_mcbond_it	1.206
r_mcbond_other	1.206
r_angle_refined_deg	1.137
r_scbond_it	1.056
r_scbond_other	1.053
r_angle_other_deg	0.421
r_symmetry_nbd_other	0.213
r_nbd_other	0.189
r_symmetry_nbd_refined	0.187
r_nbd_refined	0.186
r_nbtor_refined	0.16
r_ncsr_local_group_3	0.147
r_ncsr_local_group_1	0.132
r_ncsr_local_group_2	0.131
r_xyhbond_nbd_refined	0.106
r_symmetry_xyhbond_nbd_refined	0.084
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.05
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3376
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing