9EOD | pdb_00009eod

Human serum albumin with adamantene carboxylic acid

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	50 mM potassium phosphate pH 7.5 31 - 34 % PEG3350 Initial hollow crystals were used as seed stock for seeding experiments.

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 174.86	α = 90
b = 38.13	β = 106.152
c = 190.97	γ = 90

Symmetry
Space Group	I 1 2 1

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		2023-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

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	1.9	52.97	98	0.11	0.11	0.131	0.063	0.994	5.96	6.5		96690

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	100		1.122	1.225	0.483	0.633	1.8	6.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.9	52.97	96690	4876	99.815	0.219	0.2168	0.2177	0.2683	0.2691	39.192

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]
1.351		1.183	-1.094		-0.806

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.402
r_dihedral_angle_6_deg	15.3
r_dihedral_angle_2_deg	9.569
r_lrange_other	8.075
r_lrange_it	8.069
r_scangle_it	7.192
r_scangle_other	7.191
r_dihedral_angle_1_deg	5.722
r_mcangle_it	5.003
r_mcangle_other	5.003
r_scbond_other	4.961
r_scbond_it	4.96
r_mcbond_it	3.928
r_mcbond_other	3.919
r_angle_refined_deg	1.511
r_angle_other_deg	0.518
r_xyhbond_nbd_refined	0.389
r_nbd_refined	0.231
r_nbd_other	0.191
r_nbtor_refined	0.19
r_symmetry_nbd_other	0.186
r_symmetry_nbd_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.139
r_chiral_restr	0.079
r_ncsr_local_group_1	0.079
r_symmetry_nbtor_other	0.074
r_symmetry_xyhbond_nbd_other	0.052
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8792
Nucleic Acid Atoms
Solvent Atoms	250
Heterogen Atoms	144

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing