6YRU | pdb_00006yru

Crystal structure of FAP in the dark at 100K

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NCC

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
2.98	58.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.69	α = 90
b = 103.57	β = 90
c = 155.95	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	1.78	86	99.3	0.086	0.096	0.998	11.02	4.727		69240			34.226

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	1.78	1.9	99.4		1.132	1.269	0.512	1.03	4.838

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	5NCC	1.78	46.503	69195	3431	99.213	0.174	0.1721	0.18	0.2021	0.21	30.186

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]
0.73			0.486		-1.216

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.381
r_dihedral_angle_4_deg	15.19
r_dihedral_angle_3_deg	12.788
r_lrange_it	10.061
r_lrange_other	9.773
r_dihedral_angle_1_deg	7.482
r_scangle_it	6.17
r_scangle_other	6.169
r_scbond_other	4.613
r_scbond_it	4.61
r_mcangle_other	3.218
r_mcangle_it	3.216
r_mcbond_it	2.346
r_mcbond_other	2.339
r_angle_refined_deg	1.661
r_angle_other_deg	1.468
r_symmetry_nbd_refined	0.278
r_nbd_other	0.238
r_xyhbond_nbd_refined	0.235
r_nbd_refined	0.202
r_symmetry_xyhbond_nbd_refined	0.197
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_other	0.098
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.077
r_bond_refined_d	0.011
r_gen_planes_refined	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	525
Heterogen Atoms	93

Software

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